From 16ad03cc13a1f97e6672dfc0afd9d8d65c9cadd0 Mon Sep 17 00:00:00 2001 From: migbro Date: Wed, 1 Jul 2020 15:32:23 -0400 Subject: [PATCH 1/9] :book: added fastq split instruction for COV-IRT :hammer: added ability to use gtf instead of cache for VEP :book: updated PR template --- .github/PULL_REQUEST_TEMPLATE.md | 3 +- fq_split_rg_instructions.md | 105 +++++++++++++++++++++++++++++ tools/variant_effect_predictor.cwl | 48 ++++++++----- 3 files changed, 137 insertions(+), 19 deletions(-) create mode 100644 fq_split_rg_instructions.md diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 5f9b991..1c43c98 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -36,4 +36,5 @@ Please describe the tests that you ran to verify your changes. Provide instructi - [ ] I have added tests that prove my fix is effective or that my feature works - [ ] New and existing unit tests pass locally with my changes - [ ] Any dependent changes have been merged and published in downstream modules -- [ ] I have checked my code and corrected any misspellings \ No newline at end of file +- [ ] I have checked my code and corrected any misspellings +- [ ] Have I ensured that commits used for testing have been pushed before PR approval? \ No newline at end of file diff --git a/fq_split_rg_instructions.md b/fq_split_rg_instructions.md new file mode 100644 index 0000000..e13a172 --- /dev/null +++ b/fq_split_rg_instructions.md @@ -0,0 +1,105 @@ +# Get code and install in python env + +```sh +git clone https://github.com/kmhernan/gdc-fastq-splitter +cd gdc-fastq-splitter +``` +*if you don't have it yet*, get virtual env for python3 + +`pip3 install virtualenv # depends on your set up` + +```sh +virtualenv venv --python /usr/bin/python3 # again, wherever your python3 (should be version 3.5+) is installed +./venv/bin/pip install . +venv/bin/gdc-fastq-splitter -h # if successful, you should get help menu +``` + +# Fun time run time + +```text +inputs: + -rw-rw-r-- 1 ubuntu ubuntu 84M May 7 04:31 COVHA-P1-D06-N.filtered.human.R1.fastq.gz + -rw-rw-r-- 1 ubuntu ubuntu 88M May 7 04:31 COVHA-P1-D06-N.filtered.human.R2.fastq.gz +``` + +```sh +gdc-fastq-splitter/venv/bin/gdc-fastq-splitter COVHA-P1-D06-N.filtered.human.R1.fastq.gz COVHA-P1-D06-N.filtered.human.R2.fastq.gz -o COVHA-P1-D06-N.filtered.human_ 2> errs.log +``` + + +## Result outputs: + +```text + -rw-rw-r-- 1 ubuntu ubuntu 34M Jul 1 18:38 COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R1.fq.gz + -rw-rw-r-- 1 ubuntu ubuntu 8.9K Jul 1 18:38 COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R1.report.json + -rw-rw-r-- 1 ubuntu ubuntu 36M Jul 1 18:38 COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R2.fq.gz + -rw-rw-r-- 1 ubuntu ubuntu 8.9K Jul 1 18:38 COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R2.report.json + -rw-rw-r-- 1 ubuntu ubuntu 34M Jul 1 18:38 COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R1.fq.gz + -rw-rw-r-- 1 ubuntu ubuntu 9.6K Jul 1 18:38 COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R1.report.json + -rw-rw-r-- 1 ubuntu ubuntu 36M Jul 1 18:38 COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R2.fq.gz + -rw-rw-r-- 1 ubuntu ubuntu 9.6K Jul 1 18:38 COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R2.report.json +``` + +json outputs have relevant RG info, metadata field most relevant, early barcode field is informative + +from `COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R1.report.json` + +```json + "metadata": { + "fastq_filename": "COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R1.fq.gz", + "flowcell_barcode": "H5NKGDSXY", + "lane_number": 1, + "multiplex_barcode": "TGAACACC+CGCCTAGG", + "record_count": 494598 + } +``` + +from `COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R1.report.json` + +```json + "metadata": { + "fastq_filename": "COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R1.fq.gz", + "flowcell_barcode": "H5NKGDSXY", + "lane_number": 2, + "multiplex_barcode": "TGAACACC+CGCCTAGG", + "record_count": 488895 + } +``` + +Recommended RGs based on these two files: + +```text +@RG ID:H5NKGDSXY.1 PL:ILLUMINA PU:H5NKGDSXY.1.TGAACACC+CGCCTAGG LB:COVHA-P1-D06-N.filtered.human :COVHA-P1-D06-N.filtered.human +@RG ID:H5NKGDSXY.2 PL:ILLUMINA PU:H5NKGDSXY.1.TGAACACC+CGCCTAGG LB:COVHA-P1-D06-N.filtered.human SM:COVHA-P1-D06-N.filtered.human +``` + +# Updated STAR Command, based on [Google Drive doc](https://drive.google.com/file/d/1z7euPSE77jbthKi8ty7dscq-oNx4wgF3/view?usp=sharing) follwing instruction from [STAR manual](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf), page 8, section 3.2: + +```sh +STAR --twopassMode Basic \ + --limitBAMsortRAM 105000000000 \ +--genomeDir /path/to/STAR/genome/directory \ + --outSAMunmapped Within \ + --outFilterType BySJout \ + --outSAMattributes NH HI AS nM NM MD jM jI MC ch \ #same as All + --outSAMattrRGline ID:H5NKGDSXY.1 PL:ILLUMINA PU:H5NKGDSXY.1.TGAACACC+CGCCTAGG LB:COVHA-P1-D06-N.filtered.human SM:COVHA-P1-D06-N.filtered.human , ID:H5NKGDSXY.2 PL:ILLUMINA PU:H5NKGDSXY.1.TGAACACC+CGCCTAGG LB:COVHA-P1-D06-N.filtered.human SM:COVHA-P1-D06-N.filtered.human \ + --outFilterMultimapNmax 20 \ + --outFilterMismatchNmax 999 \ + --outFilterMismatchNoverReadLmax 0.04 \ + --alignIntronMin 20 \ + --alignIntronMax 1000000 \ + --alignMatesGapMax 1000000 \ + --alignSJoverhangMin 8 \ + --alignSJDBoverhangMin 1 \ + --sjdbScore 1 \ + --readFilesCommand zcat \ + --runThreadN 24 \ + --chimOutType Junctions \ + --chimOutJunctionFormat 1 + --chimSegmentMin 20 \ + --outSAMtype BAM SortedByCoordinate \ + --quantMode TranscriptomeSAM GeneCounts \ + --outSAMheaderHD @HD VN:1.4 SO:coordinate \ + --outFileNamePrefix /path/to/output/directory/${sample} \ + --readFilesIn COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R1.fq.gz,COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R1.fq.gz,COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R2.fq.gz,COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R2.fq.gz +``` \ No newline at end of file diff --git a/tools/variant_effect_predictor.cwl b/tools/variant_effect_predictor.cwl index 2ff8ff0..3c19768 100644 --- a/tools/variant_effect_predictor.cwl +++ b/tools/variant_effect_predictor.cwl @@ -1,7 +1,7 @@ cwlVersion: v1.0 class: CommandLineTool id: vep-1oo-annotate -doc: "VEP Release 100. Basic tool with no customization" +doc: "VEP Release 100. Basic annotation tool, can use cache or vcf" requirements: - class: ShellCommandRequirement - class: InlineJavascriptRequirement @@ -17,24 +17,20 @@ arguments: valueFrom: >- set -eo pipefail - tar -xzf - $(inputs.cache.path) - && perl /ensembl-vep/vep - --cache --dir_cache $PWD - --cache_version 100 - --vcf - --symbol ${ - if (inputs.merged_cache){ - return " --merged "; - } + if (inputs.cache){ + var cmd = "tar -xzf " + inputs.cache.path + ";"; + return cmd; + } else{ - return " "; - } + return "echo No cache skipping unzip;"; + } } + + perl /ensembl-vep/vep + --vcf --canonical --variant_class - --offline --ccds --uniprot --protein @@ -43,6 +39,7 @@ arguments: --hgvsg --fork 14 --sift b + --symbol --vcf_info_field ANN -i $(inputs.input_vcf.path) -o STDOUT @@ -52,8 +49,22 @@ arguments: --allele_number --dont_skip --allow_non_variant - --fasta $(inputs.reference.path) | - /ensembl-vep/htslib/bgzip -@ 14 -c > $(inputs.output_basename).$(inputs.tool_name).vep.vcf.gz + --fasta $(inputs.reference.path) + ${ + var args = ""; + if (inputs.cache){ + args = " --cache --dir_cache $PWD --cache_version 100 --offline "; + if (inputs.merged_cache){ + args += " --merged "; + } + } + else{ + args = " --gtf " + inputs.bgzipped_gtf.path; + } + return args; + } + | + /ensembl-vep/htslib/bgzip -@ 2 -c > $(inputs.output_basename).$(inputs.tool_name).vep.vcf.gz && /ensembl-vep/htslib/tabix $(inputs.output_basename).$(inputs.tool_name).vep.vcf.gz inputs: @@ -62,9 +73,10 @@ inputs: type: File secondaryFiles: [.tbi] output_basename: string - merged_cache: {type: boolean, doc: "If merged cache being used", default: true} + merged_cache: {type: boolean?, doc: "If merged cache being used", default: true} tool_name: {type: string, doc: "Name of tool used to generate calls"} - cache: {type: File, label: tar gzipped cache from ensembl/local converted cache} + cache: {type: File?, label: tar gzipped cache from ensembl/local converted cache, doc: "Use this if not using a gtf for gene models"} + bgzipped_gtf: {type: File?, doc: "If merged cache being used", secondaryFiles: ['.tbi'], doc: "Use this if not using a cahce, but using gtf instead for gene models"} outputs: output_vcf: From 2c53a40300e4f5ee808a621fd2d7b5b3532a26ce Mon Sep 17 00:00:00 2001 From: migbro Date: Thu, 2 Jul 2020 09:52:50 -0400 Subject: [PATCH 2/9] :bug: fixed doc error - needed space between read 1 and read 2 files --- fq_split_rg_instructions.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/fq_split_rg_instructions.md b/fq_split_rg_instructions.md index e13a172..ff9c529 100644 --- a/fq_split_rg_instructions.md +++ b/fq_split_rg_instructions.md @@ -15,6 +15,7 @@ venv/bin/gdc-fastq-splitter -h # if successful, you should get help menu ``` # Fun time run time +Note that processing paired end files will use two cores instead on one (likely a good thing). ```text inputs: @@ -101,5 +102,5 @@ STAR --twopassMode Basic \ --quantMode TranscriptomeSAM GeneCounts \ --outSAMheaderHD @HD VN:1.4 SO:coordinate \ --outFileNamePrefix /path/to/output/directory/${sample} \ - --readFilesIn COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R1.fq.gz,COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R1.fq.gz,COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R2.fq.gz,COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R2.fq.gz + --readFilesIn COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R1.fq.gz,COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R1.fq.gz COVHA-P1-D06-N.filtered.human_H5NKGDSXY_1_R2.fq.gz,COVHA-P1-D06-N.filtered.human_H5NKGDSXY_2_R2.fq.gz ``` \ No newline at end of file From e26190c78ca77585dfaec6b21ca8ff8a1af871a8 Mon Sep 17 00:00:00 2001 From: migbro Date: Wed, 15 Jul 2020 14:27:08 -0400 Subject: [PATCH 3/9] :book: Updated documentation related to VEP :hammer: changed input format for consistency --- README.md | 10 +++++----- tools/variant_effect_predictor.cwl | 4 +--- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index f366ab0..3a878c9 100644 --- a/README.md +++ b/README.md @@ -221,6 +221,7 @@ outputs: [Variant Effect Predictor](https://useast.ensembl.org/info/docs/tools/vep/index.html) is an ENSEMBL tool for annotating variants. The tool built for this repo has very basic and rigid functionality, but can be run on any of the vcf outputs from the worfklows. `tools/variant_effect_predictor.cwl`. +It can be run using a cache or a gtf - in this case a gtf was used to be able to generate gene models for both human and SARS CoV-2 Run time (n=782) COV-IRT dataset, ~6 minutes, cost on cavatica ~$0.22 per sample @@ -235,13 +236,12 @@ Run time (n=782) COV-IRT dataset, ~6 minutes, cost on cavatica ~$0.22 per sampl ```yaml inputs: reference: {type: File, secondaryFiles: [.fai], label: Fasta genome assembly with index} - input_vcf: - type: File - secondaryFiles: [.tbi] + input_vcf: {type: File, secondaryFiles: [.tbi]} output_basename: string - merged_cache: {type: boolean, doc: "If merged cache being used", default: true} + merged_cache: {type: boolean?, doc: "If merged cache being used", default: true} tool_name: {type: string, doc: "Name of tool used to generate calls"} - cache: {type: File, label: tar gzipped cache from ensembl/local converted cache} + cache: {type: File?, label: tar gzipped cache from ensembl/local converted cache, doc: "Use this if not using a gtf for gene models"} + bgzipped_gtf: {type: File?, doc: "If merged cache being used", secondaryFiles: ['.tbi'], doc: "Use this if not using a cahce, but using gtf instead for gene models"} ``` ```yaml diff --git a/tools/variant_effect_predictor.cwl b/tools/variant_effect_predictor.cwl index 3c19768..06d9001 100644 --- a/tools/variant_effect_predictor.cwl +++ b/tools/variant_effect_predictor.cwl @@ -69,9 +69,7 @@ arguments: inputs: reference: {type: File, secondaryFiles: [.fai], label: Fasta genome assembly with index} - input_vcf: - type: File - secondaryFiles: [.tbi] + input_vcf: {type: File, secondaryFiles: [.tbi]} output_basename: string merged_cache: {type: boolean?, doc: "If merged cache being used", default: true} tool_name: {type: string, doc: "Name of tool used to generate calls"} From 313890bae2ac471d8662d7cd798c06970cccfc1d Mon Sep 17 00:00:00 2001 From: migbro Date: Mon, 20 Jul 2020 17:09:14 -0400 Subject: [PATCH 4/9] :tada: added STAR Fusion reference generator :hammer: added STAR Fusion, swtiched to ctat docker :handshake: ported over KFDRC arriba and star genome generate --- tools/arriba_fusion.cwl | 60 +++++++++++++++++++++++++++++++++++ tools/star_fusion_covirt.cwl | 43 +++++++++++++++++++++++++ tools/star_fusion_refgen.cwl | 42 ++++++++++++++++++++++++ tools/star_genomegenerate.cwl | 33 +++++++++++++++++++ 4 files changed, 178 insertions(+) create mode 100644 tools/arriba_fusion.cwl create mode 100644 tools/star_fusion_covirt.cwl create mode 100644 tools/star_fusion_refgen.cwl create mode 100644 tools/star_genomegenerate.cwl diff --git a/tools/arriba_fusion.cwl b/tools/arriba_fusion.cwl new file mode 100644 index 0000000..e3a700e --- /dev/null +++ b/tools/arriba_fusion.cwl @@ -0,0 +1,60 @@ +cwlVersion: v1.0 +class: CommandLineTool +id: arriba_fusion +requirements: + - class: ShellCommandRequirement + - class: DockerRequirement + dockerPull: 'kfdrc/arriba:1.1.0' + - class: InlineJavascriptRequirement + - class: ResourceRequirement + coresMin: 8 + ramMin: 64000 + +baseCommand: [/arriba_v1.1.0/arriba] +arguments: + - position: 1 + shellQuote: false + valueFrom: >- + -c $(inputs.chimeric_sam_out.path) + -x $(inputs.genome_aligned_bam.path) + -a $(inputs.reference_fasta.path) + -g $(inputs.gtf_anno.path) + -o $(inputs.outFileNamePrefix).arriba.fusions.tsv + -O $(inputs.outFileNamePrefix).arriba.discarded_fusions.tsv + -b /arriba_v1.1.0/database/blacklist_hg38_GRCh38_2018-11-04.tsv.gz + -T + -P + ${ + if(inputs.arriba_strand_flag == null){ + return "-s auto"; + } + else{ + return "-s " + inputs.arriba_strand_flag; + } + } && + /arriba_v1.1.0/draw_fusions.R + --annotation=$(inputs.gtf_anno.path) + --fusions=$(inputs.outFileNamePrefix).arriba.fusions.tsv + --alignments=$(inputs.genome_aligned_bam.path) + --cytobands=/arriba_v1.1.0/database/cytobands_hg38_GRCh38_2018-02-23.tsv + --proteinDomains=/arriba_v1.1.0/database/protein_domains_hg38_GRCh38_2018-03-06.gff3 + --output=$(inputs.outFileNamePrefix).arriba.fusions.pdf + +inputs: + genome_aligned_bam: File + genome_aligned_bai: File + chimeric_sam_out: File + reference_fasta: File + gtf_anno: File + outFileNamePrefix: string + arriba_strand_flag: ['null', string] + +outputs: + arriba_fusions: + type: File + outputBinding: + glob: "$(inputs.outFileNamePrefix).arriba.fusions.tsv" + arriba_pdf: + type: File + outputBinding: + glob: "$(inputs.outFileNamePrefix).arriba.fusions.pdf" diff --git a/tools/star_fusion_covirt.cwl b/tools/star_fusion_covirt.cwl new file mode 100644 index 0000000..d5200ba --- /dev/null +++ b/tools/star_fusion_covirt.cwl @@ -0,0 +1,43 @@ +cwlVersion: v1.0 +class: CommandLineTool +id: star_fusion +requirements: + - class: ShellCommandRequirement + - class: DockerRequirement + dockerPull: 'trinityctat/starfusion:1.9.0' + - class: InlineJavascriptRequirement + - class: ResourceRequirement + coresMin: 16 + ramMin: 64000 + +baseCommand: [tar] +arguments: + - position: 1 + shellQuote: false + valueFrom: >- + -zxf $(inputs.genome_tar.path) && + /usr/local/src/STAR-Fusion/STAR-Fusion + --genome_lib_dir ./$(inputs.genome_untar_path) + -J $(inputs.Chimeric_junction.path) + --output_dir STAR-Fusion_outdir + --examine_coding_effect + --CPU 16 && + mv STAR-Fusion_outdir/star-fusion.fusion_predictions.abridged.coding_effect.tsv $(inputs.SampleID).STAR.fusion_predictions.abridged.coding_effect.tsv && + gzip -c $(inputs.Chimeric_junction.path) > $(inputs.Chimeric_junction.basename).gz + + +inputs: + Chimeric_junction: File + genome_tar: File + genome_untar_path: {type: ['null', string], doc: "This is what the path will be when genome_tar is unpackaged", default: "GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir"} + SampleID: string + +outputs: + abridged_coding: + type: File + outputBinding: + glob: '*.fusion_predictions.abridged.coding_effect.tsv' + chimeric_junction_compressed: + type: File + outputBinding: + glob: "$(inputs.Chimeric_junction.basename).gz" diff --git a/tools/star_fusion_refgen.cwl b/tools/star_fusion_refgen.cwl new file mode 100644 index 0000000..f1939f9 --- /dev/null +++ b/tools/star_fusion_refgen.cwl @@ -0,0 +1,42 @@ +cwlVersion: v1.0 +class: CommandLineTool +id: star_fusion_ref_gen +doc: "Generatte STAR Fusion reference file from custom annotation using STAR Fusion v1.9.0" +requirements: + - class: ShellCommandRequirement + - class: DockerRequirement + dockerPull: 'trinityctat/starfusion:1.9.0' + - class: InlineJavascriptRequirement + - class: ResourceRequirement + coresMin: 8 + ramMin: 64000 + +baseCommand: [/usr/local/src/Fusion/ctat-genome-lib-builder/prep_genome_lib.pl] +arguments: + - position: 1 + shellQuote: false + valueFrom: >- + --genome_fa $(inputs.reference_genome.path) + --gtf $(inputs.gtf.path) + --pfam_db current + --dfam_db human + --max_readlength $(inputs.max_readlength) + --CPU 8 + + rm ctat_genome_lib_build_dir/*.gz + + rm -rf ctat_genome_lib_build_dir/_chkpts + + tar -czf $(inputs.new_reference_name).tgz ctat_genome_lib_build_dir + +inputs: + reference_genome: File + gtf: File + max_readlength: {type: ['null', int], doc: "Read length of library aligned", default: 150} + new_reference_name: {type: string, doc: "Name to use for newly created star fusion archive"} + +outputs: + star_fusion_reference: + type: File + outputBinding: + glob: '*.tgz' diff --git a/tools/star_genomegenerate.cwl b/tools/star_genomegenerate.cwl new file mode 100644 index 0000000..561f7da --- /dev/null +++ b/tools/star_genomegenerate.cwl @@ -0,0 +1,33 @@ +cwlVersion: v1.0 +class: CommandLineTool +id: build_star2_73a_align_ref +requirements: + - class: ShellCommandRequirement + - class: DockerRequirement + dockerPull: 'migbro/star:2.73a' + - class: InlineJavascriptRequirement + - class: ResourceRequirement + coresMin: "$(inputs.runThreadN ? inputs.runThreadN : 16)" + ramMin: 60000 + +baseCommand: [mkdir] +arguments: + - position: 1 + shellQuote: false + valueFrom: >- + $(inputs.genomeDir) && + STAR --runMode genomeGenerate --runThreadN $(inputs.runThreadN) --genomeDir $(inputs.genomeDir) --genomeFastaFiles $(inputs.genome_fa.path) --sjdbGTFfile $(inputs.gtf.path) --sjdbOverhang $(inputs.sjdbOverhang) + && tar --use-compress-program=pigz -cf $(inputs.genomeDir).tar.gz ./$(inputs.genomeDir) + +inputs: + genomeDir: string + genome_fa: File + gtf: File + runThreadN: int + sjdbOverhang: int + +outputs: + star_ref: + type: File + outputBinding: + glob: $(inputs.genomeDir).tar.gz \ No newline at end of file From 090a53f44326424c06c9062e6cfce6fe4a932c55 Mon Sep 17 00:00:00 2001 From: migbro Date: Mon, 27 Jul 2020 09:53:27 -0400 Subject: [PATCH 5/9] :hammer: changed to using gzipped refs for dbSNP, fixed star fusion refgen path --- tools/gatk_haplotypecaller_rnaseq.cwl | 2 +- tools/star_fusion_covirt.cwl | 2 +- tools/star_fusion_refgen.cwl | 4 ++-- workflows/d3b_gatk_rnaseq_snv_wf.cwl | 4 ++-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tools/gatk_haplotypecaller_rnaseq.cwl b/tools/gatk_haplotypecaller_rnaseq.cwl index ea05ad2..6c1b49b 100644 --- a/tools/gatk_haplotypecaller_rnaseq.cwl +++ b/tools/gatk_haplotypecaller_rnaseq.cwl @@ -32,7 +32,7 @@ inputs: reference_fasta: {type: File, secondaryFiles: ['.fai', '^.dict']} bqsr_bam: {type: File, secondaryFiles: ['^.bai']} genes_bed: {type: File?} - dbsnp: {type: File, secondaryFiles: ['.idx'], doc: "dbSNP reference"} + dbsnp: {type: File, secondaryFiles: ['.tbi'], doc: "dbSNP reference, gzipped tab indexed"} output_basename: string outputs: hc_called_vcf: diff --git a/tools/star_fusion_covirt.cwl b/tools/star_fusion_covirt.cwl index d5200ba..2a7c31a 100644 --- a/tools/star_fusion_covirt.cwl +++ b/tools/star_fusion_covirt.cwl @@ -1,6 +1,6 @@ cwlVersion: v1.0 class: CommandLineTool -id: star_fusion +id: star_fusion_covirt requirements: - class: ShellCommandRequirement - class: DockerRequirement diff --git a/tools/star_fusion_refgen.cwl b/tools/star_fusion_refgen.cwl index f1939f9..4eb5baa 100644 --- a/tools/star_fusion_refgen.cwl +++ b/tools/star_fusion_refgen.cwl @@ -1,7 +1,7 @@ cwlVersion: v1.0 class: CommandLineTool id: star_fusion_ref_gen -doc: "Generatte STAR Fusion reference file from custom annotation using STAR Fusion v1.9.0" +doc: "Generate STAR Fusion reference file from custom annotation using STAR Fusion v1.9.0" requirements: - class: ShellCommandRequirement - class: DockerRequirement @@ -11,7 +11,7 @@ requirements: coresMin: 8 ramMin: 64000 -baseCommand: [/usr/local/src/Fusion/ctat-genome-lib-builder/prep_genome_lib.pl] +baseCommand: [/usr/local/src/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl] arguments: - position: 1 shellQuote: false diff --git a/workflows/d3b_gatk_rnaseq_snv_wf.cwl b/workflows/d3b_gatk_rnaseq_snv_wf.cwl index 738e786..3f13e15 100644 --- a/workflows/d3b_gatk_rnaseq_snv_wf.cwl +++ b/workflows/d3b_gatk_rnaseq_snv_wf.cwl @@ -19,7 +19,7 @@ doc: |- call_bed_file: {type: File, doc: "BED or GTF intervals to make calls"} exome_flag: {type: string?, default: "Y", doc: "Whether to run in exome mode for callers. Should be Y or leave blank as default is Y. Only make N if you are certain"} knownsites: {type: 'File[]', doc: "Population vcfs, based on Broad best practices"} - dbsnp_vcf: {type: File, secondaryFiles: ['.idx']} + dbsnp_vcf: {type: File, secondaryFiles: ['.tbi']} tool_name: {type: string, doc: "description of tool that generated data, i.e. gatk_haplotypecaller"} mode: {type: ['null', {type: enum, name: select_vars_mode, symbols: ["gatk", "grep"]}], doc: "Choose 'gatk' for SelectVariants tool, or 'grep' for grep expression", default: "gatk"} ``` @@ -56,7 +56,7 @@ inputs: call_bed_file: {type: File, doc: "BED or GTF intervals to make calls"} exome_flag: {type: string?, default: "Y", doc: "Whether to run in exome mode for callers. Should be Y or leave blank as default is Y. Only make N if you are certain"} knownsites: {type: 'File[]', doc: "Population vcfs, based on Broad best practices"} - dbsnp_vcf: {type: File, secondaryFiles: ['.idx']} + dbsnp_vcf: {type: File, secondaryFiles: ['.tbi']} tool_name: {type: string, doc: "description of tool that generated data, i.e. gatk_haplotypecaller"} mode: {type: ['null', {type: enum, name: select_vars_mode, symbols: ["gatk", "grep"]}], doc: "Choose 'gatk' for SelectVariants tool, or 'grep' for grep expression", default: "gatk"} From 94e5c43c48b4ee3e4094abbb4f1e2a19c577a143 Mon Sep 17 00:00:00 2001 From: migbro Date: Wed, 19 Aug 2020 13:38:38 -0400 Subject: [PATCH 6/9] :tada: added gatk version of wf with VEP built in :tada: added vcf2maf tool --- tools/vep_vcf2maf.cwl | 63 ++++++++ workflows/d3b_gatk_rnaseq_snv_plus_vep.cwl | 175 +++++++++++++++++++++ workflows/d3b_gatk_rnaseq_snv_wf.cwl | 2 +- 3 files changed, 239 insertions(+), 1 deletion(-) create mode 100644 tools/vep_vcf2maf.cwl create mode 100644 workflows/d3b_gatk_rnaseq_snv_plus_vep.cwl diff --git a/tools/vep_vcf2maf.cwl b/tools/vep_vcf2maf.cwl new file mode 100644 index 0000000..a3d1e3b --- /dev/null +++ b/tools/vep_vcf2maf.cwl @@ -0,0 +1,63 @@ +cwlVersion: v1.0 +class: CommandLineTool +id: kfdrc-vep-somatic-annotate-maf +requirements: + - class: ShellCommandRequirement + - class: InlineJavascriptRequirement + - class: ResourceRequirement + ramMin: 24000 + coresMin: 16 + - class: DockerRequirement + dockerPull: 'kfdrc/vep:r93_v2' +baseCommand: [tar, -xzf ] +arguments: + - position: 1 + shellQuote: false + valueFrom: >- + $(inputs.cache.path) + && gunzip -c $(inputs.input_vcf.path) > input_file.vcf + && perl /vcf2maf/vcf2maf.pl + --input-vcf input_file.vcf + --output-maf $(inputs.output_basename).$(inputs.tool_name).vep.maf + --filter-vcf 0 + --vep-path /ensembl-vep/ + --vep-data $PWD + --vep-forks 16 + --ncbi-build $(inputs.ref_build) + --cache-version $(inputs.cache_version) + --ref-fasta $(inputs.reference.path) + --tumor-id $(inputs.tumor_id) + && mv input_file.vep.vcf $(inputs.output_basename).$(inputs.tool_name).PASS.vep.vcf + && /ensembl-vep/htslib/bgzip $(inputs.output_basename).$(inputs.tool_name).PASS.vep.vcf + && /ensembl-vep/htslib/tabix $(inputs.output_basename).$(inputs.tool_name).PASS.vep.vcf.gz + +inputs: + reference: {type: File, secondaryFiles: [.fai], label: Fasta genome assembly with index} + input_vcf: + type: File + secondaryFiles: [.tbi] + output_basename: string + tumor_id: string + tool_name: string + cache: { type: File, label: tar gzipped cache from ensembl/local converted cache } + cache_version: {type: ['null', int], doc: "Version being used, should match build version", default: 93} + ref_build: {type: ['null', string], doc: "Genome ref build used, should line up with cache.", default: "GRCh38" } + + +outputs: + output_vcf: + type: File + outputBinding: + glob: '*.vcf.gz' + output_tbi: + type: File + outputBinding: + glob: '*.vcf.gz.tbi' + output_maf: + type: File + outputBinding: + glob: '*.maf' + warn_txt: + type: ["null", File] + outputBinding: + glob: '*.txt' diff --git a/workflows/d3b_gatk_rnaseq_snv_plus_vep.cwl b/workflows/d3b_gatk_rnaseq_snv_plus_vep.cwl new file mode 100644 index 0000000..59409bc --- /dev/null +++ b/workflows/d3b_gatk_rnaseq_snv_plus_vep.cwl @@ -0,0 +1,175 @@ +cwlVersion: v1.0 +class: Workflow +doc: |- + GATK RNAseq SNV Calling Workflow + + The overall [workflow](https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels-) picks up from post-STAR alignment, starting at Picard mark duplicates. + For the most part, tool parameters follow defaults from the GATK Best Practices [WDL](https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels/blob/master/gatk4-rna-best-practices.wdl), written in cwl with added optimatization for use on the Cavatica platform. + The git repo serving this app and related tools can be found [here](https://github.com/d3b-center/d3b-dev-rnaseq-snv/releases/tag/0.4). + `workflows/d3b_gatk_rnaseq_snv_wf.cwl` is the wrapper cwl used to run all tools for GATK4. + + ### Inputs + ```yaml + inputs: + output_basename: string + scatter_ct: {type: int?, doc: "Number of interval lists to split into", default: 50} + STAR_sorted_genomic_bam: {type: File, doc: "STAR sorted alignment bam"} + reference_fasta: {type: File, secondaryFiles: ['^.dict', '.fai'], doc: "Reference genome used"} + reference_dict: File + call_bed_file: {type: File, doc: "BED or GTF intervals to make calls"} + exome_flag: {type: string?, default: "Y", doc: "Whether to run in exome mode for callers. Should be Y or leave blank as default is Y. Only make N if you are certain"} + knownsites: {type: 'File[]', doc: "Population vcfs, based on Broad best practices"} + dbsnp_vcf: {type: File, secondaryFiles: ['.tbi']} + tool_name: {type: string, doc: "description of tool that generated data, i.e. gatk_haplotypecaller"} + mode: {type: ['null', {type: enum, name: select_vars_mode, symbols: ["gatk", "grep"]}], doc: "Choose 'gatk' for SelectVariants tool, or 'grep' for grep expression", default: "gatk"} + ``` + + ### Outputs + ```yaml + outputs: + filtered_hc_vcf: {type: File, outputSource: gatk_filter_vcf/filtered_vcf, doc: "Haplotype called vcf with Broad-recommended FILTER values added"} + pass_vcf: {type: File, outputSource: gatk_pass_vcf/pass_vcf, doc: "Filtered vcf selected for PASS variants"} + anaylsis_ready_bam: {type: File, outputSource: gatk_applybqsr/recalibrated_bam, doc: "Duplicate marked, Split N trimmed CIGAR BAM, BQSR recalibratede, ready for RNAseq calling"} + bqsr_table: {type: File, outputSource: gatk_baserecalibrator/output, doc: "BQSR table"} + ``` + + ### Docker Pulls + - `kfdrc/sambamba:0.7.1` + - `kfdrc/gatk:4.1.7.0R` + + ### Simulated bash calls + An example of bash calls from each step can be found in the [git repo](https://github.com/d3b-center/d3b-dev-rnaseq-snv#gatk4-simulated-bash-calls) + +id: d3b-gatk-rnaseq-snv-vep-wf +label: "GATK RNAseq SNV Calling Workflow" +requirements: + - class: ScatterFeatureRequirement + - class: MultipleInputFeatureRequirement + - class: SubworkflowFeatureRequirement + +inputs: + output_basename: string + scatter_ct: {type: int?, doc: "Number of interval lists to split into", default: 50} + STAR_sorted_genomic_bam: {type: File, doc: "STAR sorted alignment bam"} + reference_fasta: {type: File, secondaryFiles: ['^.dict', '.fai'], doc: "Reference genome used"} + reference_dict: File + call_bed_file: {type: File, doc: "BED or GTF intervals to make calls"} + exome_flag: {type: string?, default: "Y", doc: "Whether to run in exome mode for callers. Should be Y or leave blank as default is Y. Only make N if you are certain"} + knownsites: {type: 'File[]', doc: "Population vcfs, based on Broad best practices"} + dbsnp_vcf: {type: File, secondaryFiles: ['.tbi']} + tool_name: {type: string, doc: "description of tool that generated data, i.e. gatk_haplotypecaller"} + mode: {type: ['null', {type: enum, name: select_vars_mode, symbols: ["gatk", "grep"]}], doc: "Choose 'gatk' for SelectVariants tool, or 'grep' for grep expression", default: "gatk"} + input_tumor_name: string + vep_cache: {type: File, doc: "Tar gzipped cache from VEP"} + vep_ref_build: {type: ['null', string], doc: "Genome ref build used, should line up with cache.", default: "GRCh38" } + + +outputs: + filtered_hc_vcf: {type: File, outputSource: gatk_filter_vcf/filtered_vcf, doc: "Haplotype called vcf with Broad-recommended FILTER values added"} + vep_pass_vcf: {type: File, outputSource: vep_annot_gatk/output_vcf, secondaryFiles: ['.tbi'], doc: "Filtered vcf selected for PASS variants"} + vep_maf: {type: File, outputSource: vep_annot_gatk/output_maf, doc: "Filtered vcf selected for PASS variants"} + anaylsis_ready_bam: {type: File, outputSource: gatk_applybqsr/recalibrated_bam, doc: "Duplicate marked, Split N trimmed CIGAR BAM, BQSR recalibratede, ready for RNAseq calling"} + bqsr_table: {type: File, outputSource: gatk_baserecalibrator/output, doc: "BQSR table"} + +steps: + bedtools_gtf_to_bed: + run: ../tools/bedtools_gtf_to_bed.cwl + in: + input_bed_gtf: call_bed_file + out: [run_bed] + gatk_intervallisttools: + run: ../tools/gatk_intervallisttool.cwl + in: + interval_list: bedtools_gtf_to_bed/run_bed + reference_dict: reference_dict + exome_flag: exome_flag + scatter_ct: scatter_ct + bands: + valueFrom: ${return 80000000} + out: [output] + preprocess_rnaseq_bam: + run: ../subworkflows/preprocess_rnaseq_bam.cwl + label: "Preprocess RNAseq BAM" + in: + STAR_sorted_genomic_bam: STAR_sorted_genomic_bam + reference_fasta: reference_fasta + out: + [sorted_md_splitn_bam] + gatk_baserecalibrator: + hints: + - class: 'sbg:AWSInstanceType' + value: c5.xlarge + run: ../tools/gatk_baserecalibrator.cwl + label: "GATK BQSR" + in: + input_bam: preprocess_rnaseq_bam/sorted_md_splitn_bam + knownsites: knownsites + reference: reference_fasta + out: [output] + gatk_applybqsr: + run: ../tools/gatk_applybqsr.cwl + label: "GATK Apply BQSR" + in: + reference: reference_fasta + input_bam: preprocess_rnaseq_bam/sorted_md_splitn_bam + bqsr_report: gatk_baserecalibrator/output + out: [recalibrated_bam] + gatk_haplotype_rnaseq: + hints: + - class: 'sbg:AWSInstanceType' + value: c5.4xlarge + run: ../tools/gatk_haplotypecaller_rnaseq.cwl + label: "GATK Haplotype Caller" + in: + reference_fasta: reference_fasta + bqsr_bam: gatk_applybqsr/recalibrated_bam + dbsnp: dbsnp_vcf + output_basename: output_basename + genes_bed: gatk_intervallisttools/output + scatter: genes_bed + out: [hc_called_vcf] + merge_hc_vcf: + run: ../tools/gatk_mergevcfs.cwl + label: "GATK Merge HC VCF" + in: + input_vcfs: gatk_haplotype_rnaseq/hc_called_vcf + reference_dict: reference_dict + output_basename: output_basename + tool_name: tool_name + out: [merged_vcf] + gatk_filter_vcf: + run: ../tools/gatk_filtervariants.cwl + label: "GATK Hard Filter VCF" + in: + reference_fasta: reference_fasta + hc_vcf: merge_hc_vcf/merged_vcf + output_basename: output_basename + out: [filtered_vcf] + gatk_pass_vcf: + run: ../tools/gatk_selectvariants.cwl + label: "GATK Select PASS" + in: + input_vcf: gatk_filter_vcf/filtered_vcf + output_basename: output_basename + tool_name: tool_name + mode: mode + out: [pass_vcf] + vep_annot_gatk: + run: ../tools/vep_vcf2maf.cwl + label: "MSKCC VEP VCF2MAF" + in: + input_vcf: gatk_pass_vcf/pass_vcf + output_basename: output_basename + tumor_id: input_tumor_name + tool_name: tool_name + reference: reference_fasta + cache: vep_cache + ref_build: vep_ref_build + out: [output_vcf, output_tbi, output_maf, warn_txt] + + +$namespaces: + sbg: https://sevenbridges.com +hints: + - class: 'sbg:maxNumberOfParallelInstances' + value: 2 \ No newline at end of file diff --git a/workflows/d3b_gatk_rnaseq_snv_wf.cwl b/workflows/d3b_gatk_rnaseq_snv_wf.cwl index 3f13e15..23a91b7 100644 --- a/workflows/d3b_gatk_rnaseq_snv_wf.cwl +++ b/workflows/d3b_gatk_rnaseq_snv_wf.cwl @@ -125,7 +125,7 @@ steps: out: [hc_called_vcf] merge_hc_vcf: run: ../tools/gatk_mergevcfs.cwl - label: "GAK Merge HC VCF" + label: "GATK Merge HC VCF" in: input_vcfs: gatk_haplotype_rnaseq/hc_called_vcf reference_dict: reference_dict From 9380711006471f23d3cd76fd2bce781ead86bbf0 Mon Sep 17 00:00:00 2001 From: migbro Date: Wed, 26 Aug 2020 14:59:49 -0400 Subject: [PATCH 7/9] :hammer: removed fusion-related tools from this repo, as it was done for co-virt. will add to repo :tada: added RANseq SNV with VEP --- LICENSE | 2 +- tools/arriba_fusion.cwl | 60 ------------------------------------ tools/star_fusion_covirt.cwl | 43 -------------------------- 3 files changed, 1 insertion(+), 104 deletions(-) delete mode 100644 tools/arriba_fusion.cwl delete mode 100644 tools/star_fusion_covirt.cwl diff --git a/LICENSE b/LICENSE index 261eeb9..8983ef0 100644 --- a/LICENSE +++ b/LICENSE @@ -186,7 +186,7 @@ same "printed page" as the copyright notice for easier identification within third-party archives. - Copyright [yyyy] [name of copyright owner] + Copyright 2020 Center for Data-Driven Discovery in Biomedicine Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/tools/arriba_fusion.cwl b/tools/arriba_fusion.cwl deleted file mode 100644 index e3a700e..0000000 --- a/tools/arriba_fusion.cwl +++ /dev/null @@ -1,60 +0,0 @@ -cwlVersion: v1.0 -class: CommandLineTool -id: arriba_fusion -requirements: - - class: ShellCommandRequirement - - class: DockerRequirement - dockerPull: 'kfdrc/arriba:1.1.0' - - class: InlineJavascriptRequirement - - class: ResourceRequirement - coresMin: 8 - ramMin: 64000 - -baseCommand: [/arriba_v1.1.0/arriba] -arguments: - - position: 1 - shellQuote: false - valueFrom: >- - -c $(inputs.chimeric_sam_out.path) - -x $(inputs.genome_aligned_bam.path) - -a $(inputs.reference_fasta.path) - -g $(inputs.gtf_anno.path) - -o $(inputs.outFileNamePrefix).arriba.fusions.tsv - -O $(inputs.outFileNamePrefix).arriba.discarded_fusions.tsv - -b /arriba_v1.1.0/database/blacklist_hg38_GRCh38_2018-11-04.tsv.gz - -T - -P - ${ - if(inputs.arriba_strand_flag == null){ - return "-s auto"; - } - else{ - return "-s " + inputs.arriba_strand_flag; - } - } && - /arriba_v1.1.0/draw_fusions.R - --annotation=$(inputs.gtf_anno.path) - --fusions=$(inputs.outFileNamePrefix).arriba.fusions.tsv - --alignments=$(inputs.genome_aligned_bam.path) - --cytobands=/arriba_v1.1.0/database/cytobands_hg38_GRCh38_2018-02-23.tsv - --proteinDomains=/arriba_v1.1.0/database/protein_domains_hg38_GRCh38_2018-03-06.gff3 - --output=$(inputs.outFileNamePrefix).arriba.fusions.pdf - -inputs: - genome_aligned_bam: File - genome_aligned_bai: File - chimeric_sam_out: File - reference_fasta: File - gtf_anno: File - outFileNamePrefix: string - arriba_strand_flag: ['null', string] - -outputs: - arriba_fusions: - type: File - outputBinding: - glob: "$(inputs.outFileNamePrefix).arriba.fusions.tsv" - arriba_pdf: - type: File - outputBinding: - glob: "$(inputs.outFileNamePrefix).arriba.fusions.pdf" diff --git a/tools/star_fusion_covirt.cwl b/tools/star_fusion_covirt.cwl deleted file mode 100644 index 2a7c31a..0000000 --- a/tools/star_fusion_covirt.cwl +++ /dev/null @@ -1,43 +0,0 @@ -cwlVersion: v1.0 -class: CommandLineTool -id: star_fusion_covirt -requirements: - - class: ShellCommandRequirement - - class: DockerRequirement - dockerPull: 'trinityctat/starfusion:1.9.0' - - class: InlineJavascriptRequirement - - class: ResourceRequirement - coresMin: 16 - ramMin: 64000 - -baseCommand: [tar] -arguments: - - position: 1 - shellQuote: false - valueFrom: >- - -zxf $(inputs.genome_tar.path) && - /usr/local/src/STAR-Fusion/STAR-Fusion - --genome_lib_dir ./$(inputs.genome_untar_path) - -J $(inputs.Chimeric_junction.path) - --output_dir STAR-Fusion_outdir - --examine_coding_effect - --CPU 16 && - mv STAR-Fusion_outdir/star-fusion.fusion_predictions.abridged.coding_effect.tsv $(inputs.SampleID).STAR.fusion_predictions.abridged.coding_effect.tsv && - gzip -c $(inputs.Chimeric_junction.path) > $(inputs.Chimeric_junction.basename).gz - - -inputs: - Chimeric_junction: File - genome_tar: File - genome_untar_path: {type: ['null', string], doc: "This is what the path will be when genome_tar is unpackaged", default: "GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir"} - SampleID: string - -outputs: - abridged_coding: - type: File - outputBinding: - glob: '*.fusion_predictions.abridged.coding_effect.tsv' - chimeric_junction_compressed: - type: File - outputBinding: - glob: "$(inputs.Chimeric_junction.basename).gz" From 5afd5e14f7a8aebfde4997403457816e85a9dd3f Mon Sep 17 00:00:00 2001 From: migbro Date: Thu, 27 Aug 2020 11:04:42 -0400 Subject: [PATCH 8/9] :hammer: removed star-fusion, updated notebook --- notebooks/RNAseq_SNV_WF_DEV.ipynb | 5981 +++-------------------------- tools/star_fusion_refgen.cwl | 42 - 2 files changed, 525 insertions(+), 5498 deletions(-) delete mode 100644 tools/star_fusion_refgen.cwl diff --git a/notebooks/RNAseq_SNV_WF_DEV.ipynb b/notebooks/RNAseq_SNV_WF_DEV.ipynb index 78e83cd..7c070a7 100644 --- a/notebooks/RNAseq_SNV_WF_DEV.ipynb +++ b/notebooks/RNAseq_SNV_WF_DEV.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -19,6 +19,31 @@ "api = sbg.Api(config=config, error_handlers=[rate_limit_sleeper, maintenance_sleeper])" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Load app into project" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# need to have converted app to json first using rabix!\n", + "import json\n", + "project = \"d3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\"\n", + "f = open('/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/kfdrc_annoFuse_wf.json', 'r')\n", + "app_raw = f.read()\n", + "app = json.loads(app_raw)\n", + "app_id = \"kfdrc-annofuse-wf\"\n", + "# Create the Workflows\n", + "a_id = (project + \"/\" + app_id)\n", + "my_app_first = api.apps.install_app(id = a_id, raw = app)" + ] + }, { "cell_type": "markdown", "metadata": {}, @@ -29,13 +54,13 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "project = \"d3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\"\n", - "task_id = \"9aeaeaf3-0e59-4c92-a709-c6bd37431294\"\n", - "out_file = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-06-22_VEP.tsv\", \"w\")\n", + "task_id = \"00210a5f-77ec-4d07-9b1d-c08e5497e24c\"\n", + "out_file = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-08-26_gatk4_rpt.tsv\", \"w\")\n", "# task_id = \"3c20cc8e-18d7-43f2-bc2c-4a76d38a88f8\"\n", "task = api.tasks.get(task_id)\n", "jobs = {}\n", @@ -82,7 +107,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -90,8 +115,8 @@ "\n", "# max desired col width\n", "max_w = 200\n", - "tsv_in = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-06-22_VEP.tsv\")\n", - "out_md = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-06-22_VEP.md\", \"w\")\n", + "tsv_in = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-08-26_gatk4_rpt.tsv\")\n", + "out_md = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-08-26_gatk4_rpt.md\", \"w\")\n", "data = []\n", "max_len = []\n", "\n", @@ -144,7 +169,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -168,42 +193,17 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Skipping job likely killed due to spot instance kill for vep-1oo-annotate from task fc616f63-b3b1-4c5e-af7b-ff7320eee644\n", - "Skipping job likely killed due to spot instance kill for vep-1oo-annotate from task f5090a20-6c22-4797-be41-7d358a7db164\n", - "Skipping job likely killed due to spot instance kill for vep-1oo-annotate from task 8a02e36f-e613-4d0d-a0f3-f1038463cca1\n", - "Skipping job likely killed due to spot instance kill for vep-1oo-annotate from task 2622d457-209a-466b-84db-1abdb677d7e6\n", - "Skipping job likely killed due to spot instance kill for vep-1oo-annotate from task cd1d9077-c5a2-4433-bc16-b74e44f02c05\n", - "Skipping job likely killed due to spot instance kill for vep-1oo-annotate from task b43b42bf-6cb2-4d08-84b3-9cd1e30d875b\n", - "Skipping job likely killed due to spot instance kill for vep-1oo-annotate from task ead6d714-32dd-4975-9272-182f5b857ca5\n", - "Skipping job likely killed due to spot instance kill for vep-1oo-annotate from task 92e3dfad-a4d7-4a31-8d01-48009bff1e76\n", - "Skipping job likely killed due to spot instance kill for vep-1oo-annotate from task f88487a0-5dc5-4169-b454-6aafbacf4f77\n", - "Skipping job likely killed due to spot instance kill for vep-1oo-annotate from task 1fb00414-01c8-4355-886b-d22f9723f3ac\n", - "Processed 0 valid tasks\n", - "Processed 100 valid tasks\n", - "Processed 200 valid tasks\n", - "Processed 300 valid tasks\n", - "Processed 400 valid tasks\n", - "Processed 500 valid tasks\n", - "Processed 600 valid tasks\n", - "Processed 700 valid tasks\n" - ] - } - ], + "outputs": [], "source": [ "project = \"d3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\"\n", - "phrase = \"VEP R100 ANNOTATE\"\n", + "phrase = \"GATK RNAseq SNV RPT\"\n", "\n", "tasks = api.tasks.query(project=project, status=\"COMPLETED\").all()\n", - "actual_out = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/cost_est/VEP_cov-irt-actual_cost.txt\", \"w\")\n", + "actual_out = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/cost_est/gatk4_rpt_cov-irt-actual_cost.txt\", \"w\")\n", "actual_out.write(\"Task name\\tTask ID\\tCost\\tRun Time in hours\\n\")\n", - "step_run = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/cost_est/VEP_cov-irt_step_run_times.txt\", \"w\")\n", + "step_run = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/cost_est/gatk4_rpt_cov-irt_step_run_times.txt\", \"w\")\n", "step_run.write(\"Run step\\tRun time in hours\\n\")\n", "# for task in tasks:\n", "# result = get_job_run_time(task, phrase)\n", @@ -212,7 +212,7 @@ "# actual_out.write(\"\\t\".join(result[0:4]) + \"\\n\")\n", "# for step in result[4]:\n", "# step_run.write(\"\\t\".join(step) + \"\\n\")\n", - "x = 0\n", + "x = 1\n", "m = 100\n", "with concurrent.futures.ThreadPoolExecutor(16) as executor:\n", " results = {executor.submit(get_job_run_time, task, phrase): task for task in tasks}\n", @@ -240,7 +240,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -261,133 +261,12 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb671e4b0a6d31133e684\tCOVWC-20200312-P2-E02-P.all-reads_Aligned.sortedByCoord.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200312-P2-E02-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb672e4b0a6d31133e6a7\tCOVWC-20200312-P2-E02-P.all-reads_ReadsPerGene.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200312-P2-E02-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb672e4b0a6d31133e693\tCOVWC-20200312-P2-E02-P.all-reads_Chimeric.out.junction\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200312-P2-E02-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb673e4b0a6d31133e6e2\tCOVWC-20200313-P4-C01-P.all-reads_Log.final.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-C01-P\tPositive\n", - "Could not process 5eebb672e4b0a6d31133e6a2\tCOVWC-20200312-P2-E02-P.all-reads_Log.progress.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200312-P2-E02-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb673e4b0a6d31133e6d3\tCOVWC-20200313-P4-C01-P.all-reads_Aligned.sortedByCoord.out.bam.bai\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-C01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb672e4b0a6d31133e698\tCOVWC-20200312-P2-E02-P.all-reads_Log.final.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200312-P2-E02-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb672e4b0a6d31133e69d\tCOVWC-20200312-P2-E02-P.all-reads_Log.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200312-P2-E02-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb671e4b0a6d31133e689\tCOVWC-20200312-P2-E02-P.all-reads_Aligned.sortedByCoord.out.bam.bai\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200312-P2-E02-P\tPositive\n", - "Could not process 5eebb673e4b0a6d31133e6e7\tCOVWC-20200313-P4-C01-P.all-reads_Log.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-C01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb674e4b0a6d31133e6f6\tCOVWC-20200313-P4-C01-P.all-reads_SJ.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-C01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb674e4b0a6d31133e6f1\tCOVWC-20200313-P4-C01-P.all-reads_ReadsPerGene.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-C01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb673e4b0a6d31133e6dd\tCOVWC-20200313-P4-C01-P.all-reads_Chimeric.out.junction\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-C01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb673e4b0a6d31133e6d8\tCOVWC-20200313-P4-C01-P.all-reads_Aligned.toTranscriptome.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-C01-P\tPositive\n", - "Could not process 5eebb674e4b0a6d31133e6ec\tCOVWC-20200313-P4-C01-P.all-reads_Log.progress.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-C01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb673e4b0a6d31133e6ce\tCOVWC-20200313-P4-C01-P.all-reads_Aligned.sortedByCoord.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-C01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb672e4b0a6d31133e6ac\tCOVWC-20200312-P2-E02-P.all-reads_SJ.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200312-P2-E02-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb676e4b0a6d31133e740\tCOVWC-20200313-P4-D01-P.all-reads_SJ.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-D01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb671e4b0a6d31133e68e\tCOVWC-20200312-P2-E02-P.all-reads_Aligned.toTranscriptome.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200312-P2-E02-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb676e4b0a6d31133e72c\tCOVWC-20200313-P4-D01-P.all-reads_Log.final.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-D01-P\tPositive\n", - "Could not process 5eebb675e4b0a6d31133e722\tCOVWC-20200313-P4-D01-P.all-reads_Aligned.toTranscriptome.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-D01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb677e4b0a6d31133e762\tCOVWC-20200313-P4-F01-N.all-reads_Aligned.sortedByCoord.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-F01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb678e4b0a6d31133e771\tCOVWC-20200313-P4-F01-N.all-reads_Chimeric.out.junction\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-F01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb678e4b0a6d31133e77b\tCOVWC-20200313-P4-F01-N.all-reads_Log.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-F01-N\tNegative\n", - "Could not process 5eebb678e4b0a6d31133e776\tCOVWC-20200313-P4-F01-N.all-reads_Log.final.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-F01-N\tNegative\n", - "Could not process 5eebb677e4b0a6d31133e76c\tCOVWC-20200313-P4-F01-N.all-reads_Aligned.toTranscriptome.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-F01-N\tNegative\n", - "Could not process 5eebb677e4b0a6d31133e767\tCOVWC-20200313-P4-F01-N.all-reads_Aligned.sortedByCoord.out.bam.bai\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-F01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb676e4b0a6d31133e731\tCOVWC-20200313-P4-D01-P.all-reads_Log.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-D01-P\tPositive\n", - "Could not process 5eebb675e4b0a6d31133e718\tCOVWC-20200313-P4-D01-P.all-reads_Aligned.sortedByCoord.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-D01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb678e4b0a6d31133e78a\tCOVWC-20200313-P4-F01-N.all-reads_SJ.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-F01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67ae4b0a6d31133e7c7\tCOVWC-20200313-P4-G01-N.all-reads_Log.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-G01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb679e4b0a6d31133e7ae\tCOVWC-20200313-P4-G01-N.all-reads_Aligned.sortedByCoord.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-G01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb679e4b0a6d31133e7bd\tCOVWC-20200313-P4-G01-N.all-reads_Chimeric.out.junction\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-G01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67ae4b0a6d31133e7c2\tCOVWC-20200313-P4-G01-N.all-reads_Log.final.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-G01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67ae4b0a6d31133e7cc\tCOVWC-20200313-P4-G01-N.all-reads_Log.progress.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-G01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb676e4b0a6d31133e727\tCOVWC-20200313-P4-D01-P.all-reads_Chimeric.out.junction\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-D01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb679e4b0a6d31133e7b8\tCOVWC-20200313-P4-G01-N.all-reads_Aligned.toTranscriptome.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-G01-N\tNegative\n", - "Could not process 5eebb679e4b0a6d31133e7b3\tCOVWC-20200313-P4-G01-N.all-reads_Aligned.sortedByCoord.out.bam.bai\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-G01-N\tNegative\n", - "Could not process 5eebb676e4b0a6d31133e736\tCOVWC-20200313-P4-D01-P.all-reads_Log.progress.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-D01-P\tPositive\n", - "Could not process 5eebb678e4b0a6d31133e780\tCOVWC-20200313-P4-F01-N.all-reads_Log.progress.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-F01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb678e4b0a6d31133e785\tCOVWC-20200313-P4-F01-N.all-reads_ReadsPerGene.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-F01-N\tNegative\n", - "Could not process 5eebb676e4b0a6d31133e73b\tCOVWC-20200313-P4-D01-P.all-reads_ReadsPerGene.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-D01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb675e4b0a6d31133e71d\tCOVWC-20200313-P4-D01-P.all-reads_Aligned.sortedByCoord.out.bam.bai\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-D01-P\tPositive\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67ae4b0a6d31133e7d6\tCOVWC-20200313-P4-G01-N.all-reads_SJ.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-G01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67ce4b0a6d31133e80c\tCOVWC-20200313-P4-H01-N.all-reads_Log.final.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-H01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67ce4b0a6d31133e816\tCOVWC-20200313-P4-H01-N.all-reads_Log.progress.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-H01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67be4b0a6d31133e802\tCOVWC-20200313-P4-H01-N.all-reads_Aligned.toTranscriptome.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-H01-N\tNegative\n", - "Could not process 5eebb67be4b0a6d31133e7fd\tCOVWC-20200313-P4-H01-N.all-reads_Aligned.sortedByCoord.out.bam.bai\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-H01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67ce4b0a6d31133e81b\tCOVWC-20200313-P4-H01-N.all-reads_ReadsPerGene.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-H01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67ce4b0a6d31133e820\tCOVWC-20200313-P4-H01-N.all-reads_SJ.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-H01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67ce4b0a6d31133e807\tCOVWC-20200313-P4-H01-N.all-reads_Chimeric.out.junction\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-H01-N\tNegative\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67ce4b0a6d31133e811\tCOVWC-20200313-P4-H01-N.all-reads_Log.out\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-H01-N\tNegative\n", - "Could not process 5eebb67be4b0a6d31133e7f8\tCOVWC-20200313-P4-H01-N.all-reads_Aligned.sortedByCoord.out.bam\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-H01-N\tNegative\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "No relevant changes were detected in order to update the resource on the server.\n", - "Could not process 5eebb67ae4b0a6d31133e7d1\tCOVWC-20200313-P4-G01-N.all-reads_ReadsPerGene.out.tab\td3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\tCOVWC-20200313-P4-G01-N\tNegative\n" - ] - } - ], + "outputs": [], "source": [ "project = \"d3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\"\n", - "manifest = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/manifests/covwc_to_tag.txt\")\n", + "manifest = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/rsem_amnifest_to_tag.tsv\")\n", "head = next(manifest)\n", "header = head.rstrip(\"\\n\").split(\"\\t\")\n", "x = 1\n", @@ -409,23 +288,21 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "def get_gatk_refs(api, project):\n", " try:\n", " ref_dict = {}\n", - " ref_dict['reference_fasta'] = api.files.get('5eebc5d1e4b0a6d311357eb9')\n", - " ref_dict['reference_dict'] = api.files.get('5eecb14ae4b0efd899f474da')\n", + " ref_dict['reference_fasta'] = api.files.get('5f185f0de4b09d9af8ae456e')\n", + " ref_dict['reference_dict'] = api.files.get('5f185f09e4b09d9af8ae4569')\n", " known_sites = []\n", - " known_sites.append(api.files.get('5eecd8c3e4b0efd899f4ae44'))\n", - " known_sites.append(api.files.get('5eecd846e4b0efd899f4ae27'))\n", - " known_sites.append(api.files.get('5eecd846e4b0efd899f4ae26'))\n", - " known_sites.append(api.files.get('5eecd846e4b0efd899f4ae21'))\n", + " known_sites.append(api.files.get('5f161613e4b0efd84a0fd4b8'))\n", + " known_sites.append(api.files.get('5f1615e3e4b0efd84a0fd4a9'))\n", " ref_dict['knownsites'] = known_sites\n", - " ref_dict['call_bed_file'] = api.files.get('5eebdeece4b0efd899f43eaa')\n", - " ref_dict['dbsnp_vcf'] = api.files.get('5eecd846e4b0efd899f4ae24')\n", + " ref_dict['call_bed_file'] = api.files.get('5f186055e4b09d9af8ae4585')\n", + " ref_dict['dbsnp_vcf'] = api.files.get('5f161572e4b0efd84a0fd49f')\n", " ref_dict['tool_name'] = 'STAR_GATK4'\n", " except Exception as e:\n", " sys.stderr.write(str(e) + \"\\nFailed to get REFS\\n\")\n", @@ -435,7 +312,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -446,7 +323,7 @@ " input_dict[key] = ref_obj[key]\n", " info = in_file.rstrip('\\n').split('\\t')\n", " input_dict['STAR_sorted_genomic_bam'] = api.files.get(info[0])\n", - " task_name = \"GATK RNAseq SNV: \" + info[3]\n", + " task_name = \"GATK RNAseq SNV RPT: \" + info[3]\n", " task = api.tasks.create(name=task_name, project=project, app=app_name, inputs=input_dict, run=False)\n", " task.inputs['output_basename'] = task.id\n", " task.save()\n", @@ -457,13 +334,13 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "project = 'd3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study'\n", "app_name = project + \"/d3b-gatk-rnaseq-snv-wf\"\n", - "manifest = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/manifests/bams_for_gatk_to_run.tsv\")\n", + "manifest = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-08-10_bam_list.tsv\")\n", "head = next(manifest)\n", "ref_obj = get_gatk_refs(api, project)\n", "x = 1\n", @@ -485,16 +362,18 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "def get_vep_refs(api, project):\n", " try:\n", " ref_dict = {}\n", - " ref_dict['reference'] = api.files.get('5eebc5d1e4b0a6d311357eb9')\n", - " ref_dict['cache'] = api.files.get('5eed0f54e4b0efd899f4afda')\n", - " ref_dict['merged_cache'] = True\n", + " ref_dict['reference'] = api.files.get('5f185f0de4b09d9af8ae456e')\n", + " # un comment for using cache\n", + " # ref_dict['cache'] = api.files.get('5eed0f54e4b0efd899f4afda')\n", + " # ref_dict['merged_cache'] = True\n", + " ref_dict['bgzipped_gtf'] = api.files.get('5f3550c2e4b0efd8002a853b')\n", " ref_dict['tool_name'] = 'STAR_GATK4'\n", " except Exception as e:\n", " sys.stderr.write(str(e) + \"\\nFailed to get REFS\\n\")\n", @@ -504,7 +383,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -515,7 +394,7 @@ " input_dict[key] = ref_obj[key]\n", " info = in_file.rstrip('\\n').split(',')\n", " input_dict['input_vcf'] = api.files.get(info[0])\n", - " task_name = \"VEP R100 ANNOTATE: \" + info[3]\n", + " task_name = \"VEP R100 GTF ANNOTATE RPT: \" + info[sidx]\n", " task = api.tasks.create(name=task_name, project=project, app=app_name, inputs=input_dict, run=False)\n", " task.inputs['output_basename'] = task.id\n", " task.save()\n", @@ -526,14 +405,16 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "project = 'd3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study'\n", "app_name = project + \"/vep-1oo-annotate\"\n", - "manifest = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/manifests/vcf_to_annotate-manifest.csv\")\n", + "manifest = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-08_manifests/vcf-manifest.csv\")\n", "head = next(manifest)\n", + "header = head.rstrip('\\n').split(',')\n", + "sidx = header.index('sample_id')\n", "ref_obj = get_vep_refs(api, project)\n", "x = 1\n", "m = 250\n", @@ -542,7 +423,257 @@ " for result in concurrent.futures.as_completed(results):\n", " if x % m == 0:\n", " sys.stderr.write('Processed ' + str(x) + ' tasks\\n')\n", - " sys.stderr.flush()\n" + " sys.stderr.flush()\n", + " x += 1\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Run STAR Fusion" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "def get_sf_refs(api, project):\n", + " try:\n", + " ref_dict = {}\n", + " ref_dict['genome_tar'] = api.files.get('5f19e9cee4b0a6d31720b606')\n", + " ref_dict['genome_untar_path'] = 'ctat_genome_lib_build_dir'\n", + " except Exception as e:\n", + " sys.stderr.write(str(e) + \"\\nFailed to get REFS\\n\")\n", + " exit(1)\n", + " return ref_dict" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "def draft_sf_task(in_file):\n", + " try:\n", + " input_dict = {}\n", + " for key in ref_obj:\n", + " input_dict[key] = ref_obj[key]\n", + " info = in_file.rstrip('\\n').split(',')\n", + " input_dict['Chimeric_junction'] = api.files.get(info[0])\n", + " task_name = \"STAR FUSION: \" + info[sidx]\n", + " task = api.tasks.create(name=task_name, project=project, app=app_name, inputs=input_dict, run=False)\n", + " task.inputs['SampleID'] = task.id\n", + " task.save()\n", + " except Exception as e:\n", + " sys.stderr.write(str(e) + \"\\nfailed to set up task for \" + in_file)\n", + " exit(1)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "project = 'd3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study'\n", + "app_name = project + \"/star-fusion-covirt\"\n", + "manifest = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-08_manifests/chim_junction-manifest.csv\")\n", + "head = next(manifest)\n", + "header = head.rstrip('\\n').split(',')\n", + "sidx = header.index('sample_id')\n", + "ref_obj = get_sf_refs(api, project)\n", + "x = 1\n", + "m = 250\n", + "with concurrent.futures.ThreadPoolExecutor(16) as executor:\n", + " results = {executor.submit(draft_sf_task, line ): line for line in manifest}\n", + " for result in concurrent.futures.as_completed(results):\n", + " if x % m == 0:\n", + " sys.stderr.write('Processed ' + str(x) + ' tasks\\n')\n", + " sys.stderr.flush()\n", + " x += 1\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Run arriba" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "def get_arriba_refs(api, project):\n", + " try:\n", + " ref_dict = {}\n", + " ref_dict['reference_fasta'] = api.files.get('5f185f0de4b09d9af8ae456e')\n", + " ref_dict['gtf_anno'] = api.files.get('5f186055e4b09d9af8ae4585')\n", + " except Exception as e:\n", + " sys.stderr.write(str(e) + \"\\nFailed to get REFS\\n\")\n", + " exit(1)\n", + " return ref_dict" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "def draft_arriba_task(samp_id):\n", + " try:\n", + " input_dict = {}\n", + " for key in ref_obj:\n", + " input_dict[key] = ref_obj[key]\n", + " for key in inputs[samp_id]:\n", + " input_dict[key] = api.files.get(inputs[samp_id][key])\n", + " task_name = \"ARRIBA FUSION: \" + samp_id\n", + " task = api.tasks.create(name=task_name, project=project, app=app_name, inputs=input_dict, run=False)\n", + " task.inputs['outFileNamePrefix'] = task.id\n", + " task.save()\n", + " except Exception as e:\n", + " sys.stderr.write(str(e) + \"\\nfailed to set up task for \" + in_file)\n", + " exit(1)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "project = 'd3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study'\n", + "app_name = project + \"/arriba-fusion\"\n", + "inputs = {}\n", + "# process two manifests, chimeric_sam, genome bam + bai, \n", + "chim_sam = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-08_manifests/chimeric_sam-manifest.csv\")\n", + "head = next(chim_sam)\n", + "header = head.rstrip('\\n').split(',')\n", + "sidx = header.index('sample_id')\n", + "for line in chim_sam:\n", + " info = line.rstrip('\\n').split(',')\n", + " inputs[info[sidx]] = {}\n", + " inputs[info[sidx]]['chimeric_sam_out'] = info[0]\n", + "chim_sam.close()\n", + "ba_manifest = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-08_manifests/bam_bai.csv\")\n", + "head = next(ba_manifest)\n", + "header = head.rstrip('\\n').split(',')\n", + "sidx = header.index('sample_id')\n", + "for line in ba_manifest:\n", + " info = line.rstrip('\\n').split(',')\n", + " suffix = info[1][-3:]\n", + " inputs[info[sidx]][('genome_aligned_' + suffix)] = info[0]\n", + "ba_manifest.close()\n", + "\n", + "ref_obj = get_arriba_refs(api, project)\n", + "x = 1\n", + "m = 250\n", + "with concurrent.futures.ThreadPoolExecutor(16) as executor:\n", + " results = {executor.submit(draft_arriba_task, samp_id ): samp_id for samp_id in inputs}\n", + " for result in concurrent.futures.as_completed(results):\n", + " if x % m == 0:\n", + " sys.stderr.write('Processed ' + str(x) + ' tasks\\n')\n", + " sys.stderr.flush()\n", + " x += 1\n", + "# for samp_id in inputs:\n", + "# draft_arriba_task(samp_id)\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Run annoFuse" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "def get_af_refs(api, project):\n", + " try:\n", + " ref_dict = {}\n", + " ref_dict['FusionGenome'] = api.files.get('5f19e9cee4b0a6d31720b606')\n", + " ref_dict['genome_untar_path'] = 'ctat_genome_lib_build_dir'\n", + " except Exception as e:\n", + " sys.stderr.write(str(e) + \"\\nFailed to get REFS\\n\")\n", + " exit(1)\n", + " return ref_dict" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "def draft_annofuse_task(samp_id):\n", + " try:\n", + " input_dict = {}\n", + " for key in ref_obj:\n", + " input_dict[key] = ref_obj[key]\n", + " for key in inputs[samp_id]:\n", + " input_dict[key] = api.files.get(inputs[samp_id][key])\n", + " input_dict['sample_name'] = samp_id\n", + " task_name = \"annoFuse: \" + samp_id\n", + " task = api.tasks.create(name=task_name, project=project, app=app_name, inputs=input_dict, run=False)\n", + " task.inputs['output_basename'] = task.id\n", + " task.save()\n", + " except Exception as e:\n", + " sys.stderr.write(str(e) + \"\\nfailed to set up task for \" + in_file)\n", + " exit(1)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "project = 'd3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study'\n", + "app_name = project + \"/kfdrc-annofuse-wf\"\n", + "inputs = {}\n", + "# process two manifests, fusion files, rsem, \n", + "rsem_files = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-08-20_rsem_annfuse_manifest.tsv\")\n", + "head = next(rsem_files)\n", + "header = head.rstrip('\\n').split('\\t')\n", + "sidx = header.index('sample_id')\n", + "for line in rsem_files:\n", + " info = line.rstrip('\\n').split('\\t')\n", + " inputs[info[sidx]] = {}\n", + " inputs[info[sidx]]['rsem_expr_file'] = info[0]\n", + "rsem_files.close()\n", + "fusions = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/2020-08-20_fusion_results-manifest.csv\")\n", + "head = next(fusions)\n", + "header = head.rstrip('\\n').split(',')\n", + "sidx = header.index('sample_id')\n", + "for line in fusions:\n", + " info = line.rstrip('\\n').split(',')\n", + " key = 'arriba_output_file'\n", + " if re.search(\"STAR\", info[1]):\n", + " key = 'star_fusion_output_file'\n", + " inputs[info[sidx]][key] = info[0]\n", + "fusions.close()\n", + "\n", + "ref_obj = get_af_refs(api, project)\n", + "x = 1\n", + "m = 250\n", + "with concurrent.futures.ThreadPoolExecutor(16) as executor:\n", + " results = {executor.submit(draft_annofuse_task, samp_id ): samp_id for samp_id in inputs}\n", + " for result in concurrent.futures.as_completed(results):\n", + " if x % m == 0:\n", + " sys.stderr.write('Processed ' + str(x) + ' tasks\\n')\n", + " sys.stderr.flush()\n", + " x += 1" ] }, { @@ -554,35 +685,42 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "def add_metadata_to_outputs(task, phrase, in_key):\n", " if re.search(phrase, task.name):\n", " sys.stderr.write('Valid task found ' + task.name + '\\n')\n", - " metadata = task.inputs[in_key].metadata\n", + " metadata = {}\n", + " for key in task.inputs[in_key].metadata:\n", + " metadata[key] = task.inputs[in_key].metadata[key]\n", " for out_key in task.outputs:\n", " # pdb.set_trace()\n", " try:\n", " if type(task.outputs[out_key]) is not list:\n", " file_obj = api.files.get(task.outputs[out_key].id)\n", - " for key in metadata:\n", - " file_obj.metadata[key] = metadata[key]\n", + " file_obj.metadata = metadata\n", " file_obj.save()\n", + " try:\n", + " if task.outputs[out_key].secondary_files is not None:\n", + " file_obj = api.files.get(task.outputs[out_key].secondary_files[0].id)\n", + " file_obj.metadata = metadata\n", + " file_obj.save()\n", + " except Exception as e:\n", + " sys.stderr.write(str(e) + \"\\nError processing secondary file for \" + out_key + \" in \" + task.id + \" skipping\\n\")\n", + "\n", " else:\n", " for output in task.outputs[out_key]:\n", " if type(output) is not list:\n", " file_obj = api.files.get(output.id)\n", - " for key in metadata:\n", - " file_obj.metadata[key] = metadata[key]\n", + " file_obj.metadata = metadata\n", " file_obj.save()\n", " else:\n", " for item in output:\n", " if item is not None:\n", " file_obj = api.files.get(item.id)\n", - " for key in metadata:\n", - " file_obj.metadata[key] = metadata[key]\n", + " file_obj.metadata = metadata\n", " file_obj.save()\n", "\n", " except Exception as e:\n", @@ -592,5184 +730,97 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "You sure tag outputs with task prefix: VEP R100 ANNOTATE? Type \"YASS\" if so\n", - "YASS\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-A01-CP\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "No relevant changes were detected in order to update the resource on the server.\n", - "Skipping output_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-A01-CP due to error\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Skipping output_vcf for VEP R100 ANNOTATE: COVHA-20200311-P1-A01-CP due to error\n", - "No relevant changes were detected in order to update the resource on the server.\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-A01-CP due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-F07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-D02-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-F07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-D04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-A05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-D04-P due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-A05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-H01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-B04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-H01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-B04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-G07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-D04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-G07-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-D04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-B02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-D05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-B02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-D05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-A04-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-B02-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-A04-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-B07-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-H02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-E05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-H02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-E05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-D05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-D05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-F08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-A06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-F08-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-A06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-E01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-E01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-B05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-B05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-D06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-D06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-A04-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-G04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-G03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-G08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-G03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-G08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-D01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-E01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-E01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-C01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-C01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-D01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-D01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-C05-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-B06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-A02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-A05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-A02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-A05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-A06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-G05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-A06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-G05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-F06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-C08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-F06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-C08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-D01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-C04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-D01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-C04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-G04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-E07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-G04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-E07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-H04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-F07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-H04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-F07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-E09-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-E09-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-B07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-B07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-E02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-C05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-C02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-C05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-C02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-C01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-B04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-C01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-B04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-C05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-C05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-A02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-E01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-B08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-E01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-B08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-F03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-H06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-B07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-H06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-B07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-C04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-H03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-A01-CP\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-G02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-A05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-G02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-A05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-A05-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-B05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-A03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-B05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-A03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-E08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-C01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-D04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-C01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-G01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-H06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-G01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-H06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-B03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-E02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-B03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-E02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-B06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-A07-CN\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-B06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-E06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-G05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-D05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-G05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-D05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-F01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-H05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-H05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-E08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-C02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P7-H08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-C03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P7-H08-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-C03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-E04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-A08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-E04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-A08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-E03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-A03-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-E03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-D03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-F04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-D03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-F04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-G05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-G05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-B01-CN\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-B01-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-G06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-G02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-B01-CN\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-G02-P due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-B01-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-D03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-B03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-D03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-B03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-H03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-F01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-D04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-F01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P6-H08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-D06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P6-H08-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-D06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-G02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-G02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-H04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-H04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-H03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-F02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-F03-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-F02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-F03-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-A05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-A04-CN\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-A05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-A04-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-B01-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-D04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-B01-CN due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-D04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-D03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-B01-CN\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-D03-P due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-B01-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-A09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-C08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-A09-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-C08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-D09-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-F01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-F01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-A02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-A07-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-B03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-A07-CN due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-B03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-E03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-F05-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-F03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-H07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-F03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-E04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-B03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-E04-P due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-B03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-H01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-H05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-H01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-C09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-F02-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-C09-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-A03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-A02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-B03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-A02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-B03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-C04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-B01-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-A04-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-F08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-A04-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-C01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-D02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-C05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-D02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-C05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-A01-CP\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-G01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-F02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-E05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-F02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-E05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-H02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-H02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-F05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-F05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-H01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-H01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-B02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-B02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-C06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-H07-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-F05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-H03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-F05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-H03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-F03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-C02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-H04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-C02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-H04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-A05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-G03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-A05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-G03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-G04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-B06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-C09-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-B06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-C09-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-A08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-B07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-H01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-B07-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-H01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-G01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-D02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-G01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-D02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-A04-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-H01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-H01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-E06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-D08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-E06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-D08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-E05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-F04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-E05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-F04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-E02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-C03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-C04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-C03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-C04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-A06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-B04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-E06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-B04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-C07-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-C03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-C07-P due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-C03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-A08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-D07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-A08-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-D07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-G03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-H04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-G03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-H04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-B01-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-B05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-B01-CN due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-B05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-A03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-E05-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-A03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-C02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-F01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-C02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-F01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-H05-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-H05-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-A06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-H07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-H07-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-D05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-D05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-D04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-D04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-C03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-C03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-H01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-G08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-G08-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-D08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-D08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-B05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-B05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-F05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-F05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-F07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-C04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-G03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-C04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-G03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-G06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-C05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-G06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-C05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-G06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-A09-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-G06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-A09-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-E07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-G03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-E07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-D07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-F04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-D07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-A04-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-H03-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-A04-CN due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-H03-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-C06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-B02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-B02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-E01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-E01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-E08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-E08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-G03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-D01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-G05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-D01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-G05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-A04-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-F02-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-A04-CN due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-F02-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-H02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-G06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-A04-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-C07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-A04-CN due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-C07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-F09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-C05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-F09-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-C05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-E03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-D01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-C01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-D01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-E03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-H04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-E03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-G01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-D03-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-G01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-H05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-B05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-H05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-B05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-B02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-B08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-B02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-B08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-E03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-C03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-E03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-C03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-C04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-D03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-C04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-D03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-E03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-H05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-E03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-H05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-G06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-D08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-G06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-D08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-C06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-D07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-G07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-D07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-A09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-H05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-A09-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-H05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-E02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-D08-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-E02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-G02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-F02-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-G02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-D03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-E03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-D05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-A01-CP\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-D05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-F02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-F07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-F02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-F07-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-D06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-D06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-C02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-C02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-D07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-D02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-D02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-D03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-E04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-E04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-A02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-A02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-E01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-H02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-H06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-H02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-H06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-G04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-G04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-E06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-E06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-C04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-B03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-B04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-D03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-B04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-D03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P9-H08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-B09-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P9-H08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-C01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-G03-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-C01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-G03-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-E07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-C04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-E07-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-C04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-E04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-E04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-B05-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-F05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-B03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-F05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-B03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-G01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-D06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-G01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-D06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-E04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-E04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-F04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-F04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-F08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-F08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-E09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-D02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-G04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-D02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-G04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-F03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-D02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-E04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-A03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-A05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-A03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-A05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-B04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-H02-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-B04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-E05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-D09-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-E05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-D09-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-B05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-F06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-B05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-F06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-E05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-E08-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-E05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-B02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-H03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-B02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-H03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-C03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-F05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-C03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-F05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-E02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-F06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-E02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-F06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-H04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-H04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-B07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-E05-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-B07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-G04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-E09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-D01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-E09-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-D01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-A03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-D02-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-A03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-D02-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-H08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-H08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-E01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-D05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-G02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-D05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-G02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-A08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-B06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-C02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-C02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-H07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-H07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-E05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-C02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-A01-CP\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-F08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-E05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-F03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-B06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-B06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-A10-CP\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-G04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-C07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-G04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-C07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E12-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-C05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-E12-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-C05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-B01-CN\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-B01-CN due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-E06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-E06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-D01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-D01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-D03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-D03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-C06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-C07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-D05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-B04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-F04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-B04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-D05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-E04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-F01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-A03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E09-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-A03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-E09-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-A01-CP\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-A04-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C03-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-A04-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-B10-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-C06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-G01-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-C06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-D05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-B05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-D05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-B05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-D03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-F03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-B03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-F03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-B03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-E07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-G05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-E07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-F08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-F08-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-G08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-G08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-G07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-G07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-B09-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-E02-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P9-E02-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-D06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-G07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P12-C08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-G07-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P12-C08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-G04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-H06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-G04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-H06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-D02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-A05-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-D02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D09-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-H07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-E02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-H07-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-E02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-A01-CP\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-B04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-F03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-B04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-F03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-A06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-A06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-E03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-E03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-G03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-G03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-E05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-B03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-B03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-F05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-F05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-H02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-H02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-H10-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-H10-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-D09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-E01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-D01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-E01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P9-D01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-F07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-A06-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-F07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-B01-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-E04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-C01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-C01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-B06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-B06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-C04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-C04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-G07-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-A07-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-H06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F09-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-H06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-E07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-E07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-C06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-C06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-A03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-G05-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-H03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-H03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-H03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F06-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-H03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-H05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-A04-CN\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-H05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-D06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-H03-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-D06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-G03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-F04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-H05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-F04-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-H03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-B06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-G06-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-B06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C12-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-F09-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-C12-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-F09-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-B01-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-F09-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-B01-CN due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-F09-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-B06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-B06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-G02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-G02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-G02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-H08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-F03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-E06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-H02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-H01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-D03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-B03-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-D03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-D09-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-C09-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-C09-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-F05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-B02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-B02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-D04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-B08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-H06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-G03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-G08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-B02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-B02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D10-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-B01-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-C03-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-B01-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F11-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-C08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-H11-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-G02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-D06-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P9-G02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-A01-CP\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-F01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-G03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-A11-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-G01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-G01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-E02-N\n", - "Valid task found VEP R100 ANNOTATE: COVWC-20200312-P2-E02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-G06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-A12-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-C05-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-A03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-E07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-A03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-E07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-A02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-G02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-A02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-C09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-E01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-C09-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P9-E01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-B05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-B04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-D01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-D02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-H05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-D08-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-H05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-A09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-C01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-A09-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-E05-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-G05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-G05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-F06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-H04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-H04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-D03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-B06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-A08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-A07-CN\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-A08-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-A07-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-H02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C10-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-H02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-C03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-C04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-C02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-A07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-G11-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-A07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-B03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-B11-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-F04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-E09-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-B01-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-H12-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-A09-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-H12-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D11-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-A03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-A03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-B07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-F04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-B07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-B07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-D02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-C02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-H08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-A08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-H08-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-A08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-G04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-D08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C11-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-D08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-H07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-E09-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-H07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-G02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-F08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-D04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-F08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-A05-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-A02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P1-A05-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-A05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-C04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-A05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-B07-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-E05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-D04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-C01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-H06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F10-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F12-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-B04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-F12-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-B04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-A02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-H04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P9-A02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-H04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-G01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-G01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-A02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-D05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-E04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-D05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-A03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-D01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-A03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-H02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D12-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E10-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-D12-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-E10-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-C06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-D02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-F04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-F03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-B12-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-F03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-H07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-A04-CP\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-C07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-A06-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-C07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-A08-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-A08-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-F07-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-G01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-G12-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-H04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-H04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-G04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-G04-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-B09-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-H01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-G01-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P9-H01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-G06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-G10-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-H04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-B07-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-H04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-F02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-A05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-F02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-A05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-A06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-C04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-G04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-E01-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P1-G04-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-H07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-B01-CN\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-H07-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-B01-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-E08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-A02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-A04-CP\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-E08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-B03-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-E08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-E01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-C02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-E01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-H01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-A03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-G08-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-G08-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-B03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-B03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-B09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-A02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-D05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-B02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-D05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P9-B02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-B04-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-E02-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P1-B04-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-B05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-E02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-B05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-E02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-G05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-B03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-G05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-B03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-E03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-E04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-A03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-E04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-A03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E07-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-D02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-B04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-C03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-F05-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P1-F05-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-C08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-B05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-C08-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-C06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-A06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-D03-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-A06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-F07-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-H03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-C07-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-H03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-G07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-G01-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-G07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-D07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-D07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-D07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-E05-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-D07-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P1-E05-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-G08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-C05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-C02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-C02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-H04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-H04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-F01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-F01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P1-E07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200311-P1-E07-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-F06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E11-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-D05-P\n", - "Valid task found VEP R100 ANNOTATE: COVWC-20200313-P4-H01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-G03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-A09-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-H02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-H04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P9-H02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-A01-CP\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-G06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P4-C05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P4-C05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-H02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-C05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-C05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-D09-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-B09-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-B09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-H05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-B08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-F06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-D01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-H04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-C07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-F08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-H01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-D06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-F02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-F02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-A01-CP\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-E03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-B04-CN\n", - "Valid task found VEP R100 ANNOTATE: COVWC-20200313-P4-D01-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-B04-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-C02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-B05-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-C02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-B05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-C05-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-B05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-B01-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-A05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-B01-CN due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-A05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-C09-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-E01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-A05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-C06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-E01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-E01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200311-P7-H09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-G02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-D07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-C06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-C06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-G07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-F05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-F01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-H03-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-F02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-C04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-F02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-C04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-D01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-A02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-D01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-A02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-D03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-E08-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-D03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-H08-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-H03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-H08-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-H03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-F03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-G01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P9-F03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-G01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-F02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-A01-CP\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P9-F02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-G03-P\n", - "Valid task found VEP R100 ANNOTATE: COVWC-20200313-P4-C01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-B02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-H02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-A07-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-E04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-A07-CN due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-F01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-F01-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-D02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-D02-N\n", - "Valid task found VEP R100 ANNOTATE: COVWC-20200313-P4-G01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-F03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-F06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-F03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-F06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-H06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-E02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-H06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-G02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-A06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-G02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-A06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-A01-CP\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-A04-CN\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-D04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-C03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-D04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-C03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-D04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-B04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-D04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-B04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-G03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-F01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-G03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-F01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-B09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-F03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-D04-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-F03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-G05-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-H01-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-C03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-F01-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-C03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-F05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-F01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-F05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-F01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-G04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-B08-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-G04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-D06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-C02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-B02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-B08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-F09-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P3-E03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200312-P2-F04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P3-E03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200312-P2-F04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C07-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-C05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200315-P10-C07-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-C05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-H03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-F05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-H03-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-F05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-D05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-H05-P\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-D05-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P1-H05-P due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P9-E04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-D01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-F09-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P9-F01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-B08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-G04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P11-G04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200316-P12-H06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-H06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-D08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-B02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-E05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-E05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-A03-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200315-P10-C09-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-D06-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-E03-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-D06-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-E03-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-B05-N\n", - "Valid task found VEP R100 ANNOTATE: COVWC-20200313-P4-F01-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-F04-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-A05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-G04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-H01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-G04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-H01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P12-E06-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-C01-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-C01-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P1-B02-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-F02-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200313-P5-A02-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P8-F02-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200313-P5-A02-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-D05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-G05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-H04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-G09-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-H04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P7-G09-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-F04-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-B06-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-F04-N due to error\n", - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-B06-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P6-H05-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200314-P6-H05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-E04-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-E04-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P7-C08-P\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200403-P2-G05-N\n", - "Valid task found VEP R100 ANNOTATE: COVHA-20200316-P11-G07-N\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "'NoneType' object has no attribute 'id'\n", - "Skipping warn_txt for VEP R100 ANNOTATE: COVHA-20200403-P2-G05-N due to error\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Valid task found VEP R100 ANNOTATE: COVHA-20200314-P8-G01-P\n" - ] - } - ], + "outputs": [], "source": [ - "prefix = 'VEP R100 ANNOTATE'\n", + "prefix = 'VEP R100 GTF ANNOTATE RPT'\n", "project = \"d3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\"\n", "key = 'input_vcf'\n", + "print(\"You sure you want to transfer input metadata to outputs with task prefix: \" + prefix + \"? Type \\\"YASS\\\" if so\")\n", + "check = input()\n", + "if check == \"YASS\":\n", + " tasks = api.tasks.query(project=project, status=\"COMPLETED\").all()\n", + " #for task in tasks:\n", + " # add_metadata_to_outputs(task, prefix, key)\n", + " x = 1\n", + " m = 250\n", + " with concurrent.futures.ThreadPoolExecutor(16) as executor:\n", + " results = {executor.submit(add_metadata_to_outputs, task, prefix, key ): task for task in tasks}\n", + "\n", + "else:\n", + " sys.stderr.write(\"User did not type YASS, skipping\\n\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Add tags to task outputs" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "def add_tags_to_outputs(task, phrase, tags):\n", + " if re.search(phrase, task.name):\n", + " sys.stderr.write('Valid task found ' + task.name + '\\n')\n", + " for out_key in task.outputs:\n", + " # pdb.set_trace()\n", + " try:\n", + " if type(task.outputs[out_key]) is not list:\n", + " file_obj = api.files.get(task.outputs[out_key].id)\n", + " file_obj.tags = tags\n", + " file_obj.save()\n", + " try:\n", + " if task.outputs[out_key].secondary_files is not None:\n", + " file_obj = api.files.get(task.outputs[out_key].secondary_files[0].id)\n", + " file_obj.tags = tags\n", + " file_obj.save()\n", + " except Exception as e:\n", + " sys.stderr.write(str(e) + \"\\nError processing secondary file for \" + out_key + \" in \" + task.id + \" skipping\\n\")\n", + "\n", + " else:\n", + " for output in task.outputs[out_key]:\n", + " if type(output) is not list:\n", + " file_obj = api.files.get(output.id)\n", + " file_obj.tags = tags\n", + " file_obj.save()\n", + " else:\n", + " for item in output:\n", + " if item is not None:\n", + " file_obj = api.files.get(item.id)\n", + " file_obj.tags = tags\n", + " file_obj.save()\n", + "\n", + " except Exception as e:\n", + " print(e)\n", + " print(\"Skipping \" + out_key + \" for \" + task.name + \" due to error\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "prefix = 'VEP R100 GTF ANNOTATE'\n", + "project = \"d3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\"\n", + "tags = ['GATK4', 'VEP', 'R100', 'GTF-ANNOTATED']\n", "print(\"You sure tag outputs with task prefix: \" + prefix + \"? Type \\\"YASS\\\" if so\")\n", "check = input()\n", "if check == \"YASS\":\n", " tasks = api.tasks.query(project=project, status=\"COMPLETED\").all()\n", - " for task in tasks:\n", - " add_metadata_to_outputs(task, prefix, key)\n", + " #for task in tasks:\n", + " # add_metadata_to_outputs(task, prefix, key)\n", + " x = 1\n", + " m = 250\n", + " with concurrent.futures.ThreadPoolExecutor(16) as executor:\n", + " results = {executor.submit(add_tags_to_outputs, task, prefix, tags ): task for task in tasks}\n", + "\n", "else:\n", " sys.stderr.write(\"User did not type YASS, skipping\\n\")" ] @@ -5783,7 +834,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -5793,17 +844,9 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Processing task: VEP R100 ANNOTATE: COVHA-20200311-P1-A01-CP\n" - ] - } - ], + "outputs": [], "source": [ "project = \"d3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\"\n", "tasks = api.tasks.query(project=project, status=\"COMPLETED\").all()\n", @@ -5815,7 +858,6 @@ " if re.search(phrase, task.name):\n", " sys.stderr.write('Processing task: ' + task.name + \"\\n\")\n", " for out_key in task.outputs:\n", - "# try:\n", " if type(task.outputs[out_key]) is not list:\n", " file_obj = task.outputs[out_key]\n", " write_to_manifest(out, file_obj, out_key, task.name)\n", @@ -5833,9 +875,6 @@ " write_to_manifest(out, task.outputs[out_key][i][j], out_key, task.name)\n", " if task.outputs[out_key][i][j].secondary_files is not None:\n", " write_to_manifest(out, task.outputs[out_key][i][j].secondary_files[0], out_key, task.name)\n", - "# except Exception as e:\n", - "# print(e)\n", - "# print(\"Skipping \" + out_key + \" for \" + task.name + \" due to error\")\n", "out.close()\n" ] }, @@ -5848,19 +887,9 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Aborting 2b233b53-4e04-4691-ba01-114e806a27b6\tGATK RNAseq SNV: COVHA-20200403-P2-B06-N\n", - "Aborting 26c0855b-3116-48fa-9f6f-680b3eadd3ef\tGATK RNAseq SNV: COVHA-20200403-P2-E04-N\n", - "Aborting 44d400a2-4d1f-464e-93cf-32668e5da436\tGATK RNAseq SNV: COVHA-20200314-P7-C08-P\n" - ] - } - ], + "outputs": [], "source": [ "import datetime\n", "import pytz\n", @@ -5904,7 +933,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -5935,7 +964,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -5959,18 +988,9 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "You sure remove outputs from failed tasks with prefix: GATK RNAseq SNV? Type \"YASS\" if so\n", - "YASS\n" - ] - } - ], + "outputs": [], "source": [ "project = \"d3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\"\n", "tasks = api.tasks.query(project=project, status=\"ABORTED\")\n", @@ -6007,64 +1027,18 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "You sure you want to rename the files in that manifest? Type \"YASS\" if so\n", - "YASS\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Renaming file with ID 5eed644ae4b03703de625f64 _1_COVHA-20200314-P7-C07-P.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv to COVHA-20200314-P7-C07-P.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv\n", - "Renaming file with ID 5eed644ae4b03703de625fd9 _1_COVHA-20200314-P7-C07-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam to COVHA-20200314-P7-C07-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam\n", - "Renaming file with ID 5eed644ae4b03703de625fe1 _1_COVHA-20200314-P7-C07-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5 to COVHA-20200314-P7-C07-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5\n", - "Renaming file with ID 5eed644ae4b03703de625fe3 _1_COVHA-20200314-P7-C07-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai to COVHA-20200314-P7-C07-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai\n", - "Renaming file with ID 5eed644ae4b0a6d3113eaae6 _1_COVHA-20200316-P11-F01-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv to COVHA-20200316-P11-F01-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv\n", - "Renaming file with ID 5eed644ae4b0a6d3113eaaf0 _1_COVHA-20200314-P6-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv to COVHA-20200314-P6-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv\n", - "Renaming file with ID 5eed644be4b0a6d3113eab01 _1_COVHA-20200314-P6-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam to COVHA-20200314-P6-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam\n", - "Renaming file with ID 5eed644be4b0a6d3113eab05 _1_COVHA-20200314-P6-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5 to COVHA-20200314-P6-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5\n", - "Renaming file with ID 5eed644be4b0a6d3113eab06 _1_COVHA-20200314-P6-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai to COVHA-20200314-P6-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai\n", - "Renaming file with ID 5eed644be4b0a6d3113eab0c _1_COVHA-20200316-P11-F01-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam to COVHA-20200316-P11-F01-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam\n", - "Renaming file with ID 5eed644be4b0a6d3113eab10 _1_COVHA-20200315-P10-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv to COVHA-20200315-P10-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv\n", - "Renaming file with ID 5eed644be4b0a6d3113eab14 _1_COVHA-20200316-P11-F01-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai to COVHA-20200316-P11-F01-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai\n", - "Renaming file with ID 5eed644be4b0a6d3113eab15 _1_COVHA-20200316-P11-F01-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5 to COVHA-20200316-P11-F01-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5\n", - "Renaming file with ID 5eed644ce4b03703de6260c1 _1_COVHA-20200315-P10-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv to COVHA-20200315-P10-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv\n", - "Renaming file with ID 5eed644ce4b03703de6260c5 _1_COVHA-20200313-P4-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv to COVHA-20200313-P4-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv\n", - "Renaming file with ID 5eed644ce4b0a6d3113eab23 _1_COVHA-20200315-P10-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam to COVHA-20200315-P10-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam\n", - "Renaming file with ID 5eed644ce4b0a6d3113eab27 _1_COVHA-20200315-P10-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai to COVHA-20200315-P10-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai\n", - "Renaming file with ID 5eed644ce4b0a6d3113eab29 _1_COVHA-20200315-P10-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5 to COVHA-20200315-P10-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5\n", - "Renaming file with ID 5eed644de4b03703de6260c9 _1_COVHA-20200313-P4-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam to COVHA-20200313-P4-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam\n", - "Renaming file with ID 5eed644de4b03703de6260cd _1_COVHA-20200313-P4-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5 to COVHA-20200313-P4-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5\n", - "Renaming file with ID 5eed644de4b03703de6260cf _1_COVHA-20200313-P4-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai to COVHA-20200313-P4-C05-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai\n", - "Renaming file with ID 5eed644de4b03703de6260d6 _1_COVHA-20200315-P10-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam to COVHA-20200315-P10-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam\n", - "Renaming file with ID 5eed644de4b03703de6260da _1_COVHA-20200315-P10-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai to COVHA-20200315-P10-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai\n", - "Renaming file with ID 5eed644de4b03703de6260dc _1_COVHA-20200315-P10-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5 to COVHA-20200315-P10-D07-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5\n", - "Renaming file with ID 5eed644de4b03703de6260ed _1_COVHA-20200403-P2-B01-CN.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv to COVHA-20200403-P2-B01-CN.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv\n", - "Renaming file with ID 5eed7130e4b0a6d3113f4126 _1_COVHA-20200403-P1-C06-P.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv to COVHA-20200403-P1-C06-P.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv\n", - "Renaming file with ID 5eed7131e4b0a6d3113f412d _1_COVHA-20200315-P9-F02-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv to COVHA-20200315-P9-F02-N.all-reads_Aligned.sortedByCoord.out.md.splitn.recal_data.csv\n", - "Renaming file with ID 5eed7131e4b0a6d3113f4131 _1_COVHA-20200403-P1-C06-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam to COVHA-20200403-P1-C06-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam\n", - "Renaming file with ID 5eed7131e4b0a6d3113f4135 _1_COVHA-20200403-P1-C06-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5 to COVHA-20200403-P1-C06-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam.md5\n", - "Renaming file with ID 5eed7131e4b0a6d3113f4137 _1_COVHA-20200403-P1-C06-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai to COVHA-20200403-P1-C06-P.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai\n", - "Renaming file with ID 5eed7131e4b0a6d3113f4148 _1_COVHA-20200315-P9-F02-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam to COVHA-20200315-P9-F02-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bam\n", - "Renaming file with ID 5eed7131e4b0a6d3113f414e _1_COVHA-20200315-P9-F02-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai to COVHA-20200315-P9-F02-N.all-reads_Aligned.sortedByCoord.out.md.splitn.aligned.duplicates_marked.recalibrated.bai\n" - ] - } - ], + "outputs": [], "source": [ - "manifest = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/manifests/to_rename-manifest.csv\")\n", + "manifest = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/to_rename.txt\")\n", "head = next(manifest)\n", "print(\"You sure you want to rename the files in that manifest? Type \\\"YASS\\\" if so\")\n", "check = input()\n", + "sep = \"\\t\"\n", "if check == \"YASS\":\n", " for line in manifest:\n", - " info = line.split(',')\n", + " info = line.split(sep)\n", " cur = api.files.get(info[0])\n", " new_name = cur.name[3:]\n", " sys.stderr.write(\"Renaming file with ID \" + cur.id + \" \" + cur.name + \" to \" + new_name + \"\\n\")\n", @@ -6072,6 +1046,101 @@ " cur.save()" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Tag outputs by task seq id" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "project = \"d3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\"\n", + "tasks = api.tasks.query(project=project, status=\"COMPLETED\").all()\n", + "manifest = open('/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/manifests/2020-06-23_UPDATED_HUMAN_MANIFEST.txt')\n", + "head = next(manifest)\n", + "header = head.rstrip('\\n').split(\"\\t\")\n", + "phrase = \"GATK RNAseq SNV RPT\"\n", + "meta_dict = {}\n", + "for entry in manifest:\n", + " info = entry.rstrip('\\n').split('\\t')\n", + " meta_dict[info[0]] = {}\n", + " for i in range(0, len(header), 1):\n", + " meta_dict[info[0]][header[i]] = info[i]\n", + "manifest.close()\n", + "for task in tasks:\n", + " if re.search(phrase, task.name):\n", + " sys.stderr.write('Processing task: ' + task.name + \"\\n\")\n", + " parts = task.name.split()\n", + " # Mason lab changed dashes to underscore\n", + " seq_id = parts[-1].replace('-','_' )\n", + " if seq_id in meta_dict:\n", + " for out_key in task.outputs:\n", + " if type(task.outputs[out_key]) is not list:\n", + " try:\n", + " file_obj = api.files.get(task.outputs[out_key].id)\n", + " file_obj.metadata = meta_dict[seq_id]\n", + " file_obj.save()\n", + " except Exception as e:\n", + " sys.stderr.write(str(e) + \"\\n\" + file_obj.name + \" probably already tagged, skipping\\n\" )\n", + " try:\n", + " if task.outputs[out_key].secondary_files is not None:\n", + " file_obj = api.files.get(task.outputs[out_key].secondary_files[0].id)\n", + " file_obj.metadata = meta_dict[seq_id]\n", + " file_obj.save()\n", + " except Exception as e:\n", + " sys.stderr.write(str(e) + \"\\nError processing secondary file for \" + out_key + \" in \" + task.id + \" skipping\\n\")\n", + "\n", + " else:\n", + " sys.stderr.write(\"Not in manifest: \" + task.name + \" \" + task.id + \"\\n\")\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Delete files by name" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "manifest = open(\"/Users/brownm28/Documents/2020-Apr-8_RNAseq_snv_dev/delme_files.txt\")\n", + "project = \"d3b-bixu/rs-vpf5jbc3-cov-irt-controlled-access-study\"\n", + "head = next(manifest)\n", + "print(\"You sure you want to delete the files in that manifest? Type \\\"YASS\\\" if so\")\n", + "check = input()\n", + "\n", + "max_j = 25\n", + "ct = 0\n", + "found = 0\n", + "fnames = []\n", + "if check == \"YASS\":\n", + " for line in manifest:\n", + " fnames.append(line.rstrip('\\n'))\n", + " ct +=1\n", + " sys.stderr.write(\"Searching for \" + str(ct) + \" files to delete\\n\")\n", + " total = len(fnames)\n", + " for i in range(0, total, max_j):\n", + " uset = i + max_j\n", + " if uset > total:\n", + " uset = total\n", + " flist = api.files.query(project=project, names=fnames[i:uset])\n", + " for fobj in flist:\n", + " sys.stderr.write(\"Deleting \" + fobj.name + \" with ID \" + fobj.id)\n", + " fobj.delete()\n", + " found += 1\n", + " sys.stderr.write(\"Deleted \" + str(found) + \" files\\n\")\n", + " " + ] + }, { "cell_type": "code", "execution_count": null, @@ -6096,7 +1165,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.3" + "version": "3.7.7" } }, "nbformat": 4, diff --git a/tools/star_fusion_refgen.cwl b/tools/star_fusion_refgen.cwl deleted file mode 100644 index 4eb5baa..0000000 --- a/tools/star_fusion_refgen.cwl +++ /dev/null @@ -1,42 +0,0 @@ -cwlVersion: v1.0 -class: CommandLineTool -id: star_fusion_ref_gen -doc: "Generate STAR Fusion reference file from custom annotation using STAR Fusion v1.9.0" -requirements: - - class: ShellCommandRequirement - - class: DockerRequirement - dockerPull: 'trinityctat/starfusion:1.9.0' - - class: InlineJavascriptRequirement - - class: ResourceRequirement - coresMin: 8 - ramMin: 64000 - -baseCommand: [/usr/local/src/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl] -arguments: - - position: 1 - shellQuote: false - valueFrom: >- - --genome_fa $(inputs.reference_genome.path) - --gtf $(inputs.gtf.path) - --pfam_db current - --dfam_db human - --max_readlength $(inputs.max_readlength) - --CPU 8 - - rm ctat_genome_lib_build_dir/*.gz - - rm -rf ctat_genome_lib_build_dir/_chkpts - - tar -czf $(inputs.new_reference_name).tgz ctat_genome_lib_build_dir - -inputs: - reference_genome: File - gtf: File - max_readlength: {type: ['null', int], doc: "Read length of library aligned", default: 150} - new_reference_name: {type: string, doc: "Name to use for newly created star fusion archive"} - -outputs: - star_fusion_reference: - type: File - outputBinding: - glob: '*.tgz' From cb9f07e40412cbae4f8a65bfaeaadb7220c9d7b9 Mon Sep 17 00:00:00 2001 From: Miguel Brown Date: Tue, 17 Sep 2024 14:28:56 -0400 Subject: [PATCH 9/9] :hammer: commit for posterity sake --- ...ract_bash_calls_from_task-checkpoint.ipynb | 145 ++++++++++++++++++ 1 file changed, 145 insertions(+) create mode 100644 notebooks/.ipynb_checkpoints/extract_bash_calls_from_task-checkpoint.ipynb diff --git a/notebooks/.ipynb_checkpoints/extract_bash_calls_from_task-checkpoint.ipynb b/notebooks/.ipynb_checkpoints/extract_bash_calls_from_task-checkpoint.ipynb new file mode 100644 index 0000000..663585d --- /dev/null +++ b/notebooks/.ipynb_checkpoints/extract_bash_calls_from_task-checkpoint.ipynb @@ -0,0 +1,145 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import sevenbridges as sbg\n", + "from sevenbridges.errors import SbgError\n", + "from sevenbridges.http.error_handlers import rate_limit_sleeper, maintenance_sleeper\n", + "import sys\n", + "import re\n", + "import pdb\n", + "import concurrent.futures\n", + "from requests import request\n", + "import json\n", + "config = sbg.Config(profile='turbo')\n", + "api = sbg.Api(config=config, error_handlers=[rate_limit_sleeper, maintenance_sleeper])" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "project = \"kfdrc-harmonization/kf-reference-pipeline\"\n", + "task_id = \"731be06c-87b2-45d0-aed9-f55330240462\"\n", + "out_file = open(\"/Users/brownm28/Documents/playground/strelka2_subwf.tsv\", \"w\")\n", + "# task_id = \"3c20cc8e-18d7-43f2-bc2c-4a76d38a88f8\"\n", + "task = api.tasks.get(task_id)\n", + "jobs = {}\n", + "temp = {}\n", + "for job in task.get_execution_details().jobs:\n", + " if job.status == \"COMPLETED\":\n", + " check = job.name.split('_')\n", + " cmd = job.command_line\n", + " if job.command_line == None:\n", + " # pdb.set_trace()\n", + " cmd = \"embedded script or task retry\"\n", + " sys.stderr.write(\"WARN: Job \" + job.name + \" had null cmd\\n\")\n", + " if check[-1] == \"s\":\n", + " key = \"_\".join(check[:-2])\n", + " if key not in temp:\n", + " jobs[job.start_time] = {}\n", + " jobs[job.start_time][key] = cmd\n", + " temp[key] = 1\n", + " else:\n", + " temp[key] += 1\n", + " else:\n", + " jobs[job.start_time] = {}\n", + " jobs[job.start_time][job.name] = cmd\n", + "out_file.write(\"Step\\tType\\tNum scatter\\tCommand\\n\")\n", + "for rtime in sorted(jobs.keys()):\n", + " for key in jobs[rtime]:\n", + " rtype = \"run step\"\n", + " sct = \"NA\"\n", + " if key in temp and temp[key] > 1:\n", + " rtype = \"scatter\"\n", + " sct = str(temp[key])\n", + " cmds = jobs[rtime][key].split('\\n')\n", + " for cmd in cmds:\n", + " out_file.write(key + \"\\t\" + rtype + \"\\t\" + sct + \"\\t\" + cmd + \"\\n\")\n", + "out_file.close()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "\n", + "# max desired col width\n", + "max_w = 200\n", + "tsv_in = open(\"/Users/brownm28/Documents/playground/strelka2_subwf.tsv\")\n", + "out_md = open(\"/Users/brownm28/Documents/playground/strelka2_subwf.md\", \"w\")\n", + "data = []\n", + "max_len = []\n", + "\n", + "\n", + "for line in tsv_in:\n", + " info = line.rstrip('\\n').split('\\t')\n", + " data.append(info)\n", + " if len(max_len) == 0:\n", + " for item in info:\n", + " max_len.append(len(item))\n", + " else:\n", + " for i in range(len(max_len)):\n", + " if len(info[i]) > max_w:\n", + " max_len[i] = max_w\n", + " elif len(info[i]) > max_len[i]:\n", + " max_len[i] = len(info[i])\n", + "# print header first\n", + "d_ct = []\n", + "for i in range(len(data[0])):\n", + " d_ct.append(len(data[0][i]))\n", + " out_md.write(\" | \" + data[0][i] + \"\".join([\" \"] * max_len[i]))\n", + " d_ct[i] += max_len[i]\n", + "out_md.write(\" |\\n\")\n", + "for i in range(len(data[0])):\n", + " out_md.write(\" | \" + \"\".join([\"-\"] * d_ct[i]))\n", + "out_md.write(\" |\\n\")\n", + "# pdb.set_trace()\n", + "for i in range(1, len(data), 1):\n", + " for j in range(len(data[i])):\n", + " d_ct = len(data[i][j]) + 2\n", + " out_md.write(\" | \" + data[i][j] + \"\".join([\" \"] * max_len[j]))\n", + " d_ct += max_len[j]\n", + " out_md.write(\" |\\n\")\n", + "out_md.close()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.7" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +}