.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:SEQTOOL_QC (A673_FFPE_RNA_0001_B23LG7FLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/356aba0b44941bdb1ff909497fd1b2/.command.log
Size: 14.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:SEQTOOL_QC (A673_FFPE_RNA_0001_B23LG7FLT4_2)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/3a845f35d2b449c4f225bd8029ff40/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
  Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/356aba0b44941bdb1ff909497fd1b2/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.dict
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/356aba0b44941bdb1ff909497fd1b2/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/3a845f35d2b449c4f225bd8029ff40/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/twist/Twist_rna_exome_AND_fusion_hg38.bed
  Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
==> STAGING COMPLETE (11 inputs)

+ mkdir A673_FFPE_RNA_0001_B23LG7FLT4_2
+ all_qc -bam A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam -beds Twist_rna_exome_AND_fusion_hg38.bed -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz -contamination_bed dbsnp_hg38_contam_sites.bed -output_folder A673_FFPE_RNA_0001_B23LG7FLT4_2 -reference ref_genome.fa -region chr20
mkdir -p A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/


cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/full_bed.bed


seqtool depth -bam A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam -bed A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth.gz
saturation_plot       -bams A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam       -region chr20       -output A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/saturation_plot.png       -threads 1 
seqtool saturation_metric       -at 1000000       -region chr20       -bam_threads 1       A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/saturation_qc.tsv 
fragment_size       -bams A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam       -region chr20       -output_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/fragsize       -threads 1 
samtools mpileup   -B --min-MQ 60 --min-BQ 30    -f ref_genome.fa   -l dbsnp_hg38_contam_sites.bed   A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_2.md.mpileup && contamination -input A673_FFPE_RNA_0001_B23LG7FLT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/contamination.tsv 
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
/opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources
/opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai

0it [00:00, ?it/s]
113865it [00:00, 1138558.79it/s]
229886it [00:00, 1151249.82it/s]
345011it [00:00, 1142600.56it/s]
460178it [00:00, 1145983.63it/s]
575926it [00:00, 1150094.44it/s]
691481it [00:00, 1151925.46it/s]
807399it [00:00, 1154272.68it/s]
923642it [00:00, 1156833.26it/s]
1039856it [00:00, 1158473.34it/s]
1156302it [00:01, 1160302.23it/s]
1272334it [00:01, 1156482.37it/s]
1389141it [00:01, 1159981.24it/s]
1505143it [00:01, 1155435.76it/s]
1621232it [00:01, 1157061.20it/s]
1737286it [00:01, 1158091.45it/s]
1853751it [00:01, 1160047.07it/s]
1970371it [00:01, 1161876.73it/s]
2086827it [00:01, 1162665.09it/s]
2203096it [00:01, 1161932.08it/s]
2319291it [00:02, 1150357.61it/s]
2434353it [00:02, 1149596.00it/s]
2549331it [00:02, 1147926.65it/s]
2665050it [00:02, 1150681.74it/s]
2780129it [00:02, 1147286.29it/s]
2894866it [00:02, 1147166.22it/s]
3010199it [00:02, 1148994.13it/s]
3126210it [00:02, 1152310.11it/s]
3241445it [00:02, 1150213.91it/s]
3356628it [00:02, 1150686.40it/s]
3472087it [00:03, 1151844.32it/s]
3587274it [00:03, 1151388.42it/s]
3702578it [00:03, 1151774.23it/s]
3818144it [00:03, 1152923.65it/s]
3934216it [00:03, 1155248.26it/s]
4052353it [00:03, 1163068.44it/s]
4168661it [00:03, 1161428.76it/s]
4284805it [00:03, 1151770.11it/s]
4400001it [00:03, 1149530.42it/s]
4516761it [00:03, 1154901.43it/s]
4632263it [00:04, 1152365.06it/s]
4748546it [00:04, 1155474.95it/s]
4864562it [00:04, 1156742.69it/s]
4981288it [00:04, 1159874.34it/s]
5098492it [00:04, 1163502.61it/s]
5215095it [00:04, 1164240.32it/s]
5331522it [00:04, 1157983.98it/s]
5447753it [00:04, 1159259.14it/s]
5563743it [00:04, 1159432.12it/s]
5679728it [00:04, 1159538.51it/s]
5795695it [00:05, 1159562.50it/s]
5911654it [00:05, 1156996.02it/s]
6027613it [00:05, 1157754.58it/s]
6144960it [00:05, 1162441.95it/s]
6261207it [00:05, 1155232.30it/s]
6376742it [00:05, 1151848.31it/s]
6491936it [00:05, 1150526.71it/s]
6606995it [00:05, 1146921.12it/s]
6723595it [00:05, 1152560.75it/s]
6838858it [00:05, 1147500.86it/s]
6953616it [00:06, 1145772.30it/s]
7070141it [00:06, 1151575.92it/s]
7185712it [00:06, 1152801.30it/s]
7301433it [00:06, 1154109.34it/s]
7418053it [00:06, 1157716.32it/s]
7533828it [00:06, 1157266.27it/s]
7649557it [00:06, 1149137.88it/s]
7764485it [00:06, 1148824.39it/s]
7880728it [00:06, 1152792.20it/s]
7997883it [00:06, 1158300.38it/s]
8114930it [00:07, 1161870.65it/s]
8231123it [00:07, 1159242.12it/s]
8347053it [00:07, 1155133.24it/s]
8463713it [00:07, 1158541.20it/s]
8579573it [00:07, 1157754.22it/s]
8695415it [00:07, 1157936.41it/s]
8811212it [00:07, 1157748.43it/s]
8928449it [00:07, 1162112.38it/s]
9044663it [00:07, 1159835.32it/s]
9162061it [00:07, 1164051.94it/s]
9278469it [00:08, 1160205.09it/s]
9394494it [00:08, 1158963.05it/s]
9510394it [00:08, 1156037.46it/s]
9627140it [00:08, 1159434.51it/s]
9743087it [00:08, 1158749.54it/s]
9858965it [00:08, 1153714.93it/s]
9974342it [00:08, 1151837.54it/s]
10089530it [00:08, 1148543.16it/s]
10204388it [00:08, 1147601.49it/s]
10319151it [00:08, 1145578.58it/s]
10434220it [00:09, 1147096.15it/s]
10548932it [00:09, 1141536.76it/s]
10663092it [00:09, 1140203.86it/s]
10778106it [00:09, 1143158.97it/s]
10893254it [00:09, 1145636.02it/s]
11008680it [00:09, 1148207.78it/s]
11124337it [00:09, 1150697.12it/s]
11242089it [00:09, 1158721.91it/s]
11357964it [00:09, 1156095.78it/s]
11476392it [00:09, 1164516.53it/s]
11592848it [00:10, 1162464.36it/s]
11709098it [00:10, 1161237.33it/s]
11825829it [00:10, 1163039.39it/s]
11942581it [00:10, 1164365.05it/s]
12059020it [00:10, 1161944.78it/s]
12175833it [00:10, 1163781.49it/s]
12292213it [00:10, 1161383.08it/s]
12408354it [00:10, 1156610.58it/s]
12524020it [00:10, 1155173.35it/s]
12641129it [00:10, 1159815.63it/s]
12757115it [00:11, 1158717.85it/s]
12872990it [00:11, 1157497.62it/s]
12988778it [00:11, 1157595.84it/s]
13104591it [00:11, 1157729.67it/s]
13220434it [00:11, 1157924.93it/s]
13336343it [00:11, 1158258.73it/s]
13452657it [00:11, 1159706.71it/s]
13568973it [00:11, 1160725.11it/s]
13685220it [00:11, 1161232.12it/s]
13801344it [00:11, 1158628.33it/s]
13917209it [00:12, 1157004.42it/s]
14032911it [00:12, 1156337.66it/s]
14148546it [00:12, 1150623.22it/s]
14263726it [00:12, 1150962.59it/s]
14378827it [00:12, 1148631.29it/s]
14494067it [00:12, 1149747.28it/s]
14564283it [00:12, 1155100.79it/s]
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai




[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai


[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai


tabix -s 1 -b 2 -e 2 A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth.gz


seqtool depth_hist     -nbins 500     A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth.gz     > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth_hist.tsv


cat A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth_hist.tsv | plot         -x 0         -xlabel Depth -ylabel "Number of Sites"         -xlim 0 2000         -title A673_FFPE_RNA_0001_B23LG7FLT4_2.md         -output A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth.png


[W::hts_idx_load3] The index file is older than the data file: Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi


seqtool read_qc    -bed Twist_rna_exome_AND_fusion_hg38.bed     -n_threads 1     -bam_threads 2     A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/read_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool reads_per_target     -bed Twist_rna_exome_AND_fusion_hg38.bed     -threads 1     -bam_threads 2     A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv 
seqtool depth_stats  -bed Twist_rna_exome_AND_fusion_hg38.bed  A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth.gz> A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/depth_stats.Twist_rna_exome_AND_fusion_hg38.bed.tsv 
seqtool gc_bias  -reference ref_genome.fa  -bed Twist_rna_exome_AND_fusion_hg38.bed  -bin_size 0.05  -threads 1  -bam_threads 2  A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam  > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv 
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai




cat A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "A673_FFPE_RNA_0001_B23LG7FLT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 






echo `date` > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/qc_complete.txt


+ merge_qc -folders A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md -output A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2_full_basic_stats.tsv
+ head -n1 A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2_full_basic_stats.tsv