Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/28a94f0ccb3fdcb88082a2f5cce61b/659_bKP-T1-TRNA-1_B23MHV2LT4_1.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/85/eb07d8700075ed33bfa92530126000/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/28a94f0ccb3fdcb88082a2f5cce61b/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
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/85/eb07d8700075ed33bfa92530126000/.command.run
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 659_bKP-T1-TRNA-1_B23MHV2LT4_1
+ all_qc -bam 659_bKP-T1-TRNA-1_B23MHV2LT4_1.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 659_bKP-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20
mkdir -p 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed
seqtool depth -bam 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz
saturation_plot -bams 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv
fragment_size -bams 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.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: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
0it [00:00, ?it/s]
153090it [00:00, 1530802.92it/s]
318446it [00:00, 1602962.52it/s]
485865it [00:00, 1635443.47it/s]
655119it [00:00, 1657948.50it/s]
823968it [00:00, 1668930.61it/s]
992689it [00:00, 1675111.99it/s]
1160201it [00:00, 1673311.41it/s]
1330733it [00:00, 1683466.10it/s]
1499081it [00:00, 1678900.99it/s]
1668562it [00:01, 1683636.21it/s]
1836929it [00:01, 1682520.59it/s]
2005534it [00:01, 1683563.79it/s]
2174984it [00:01, 1686782.24it/s]
2343664it [00:01, 1685661.29it/s]
2512232it [00:01, 1683904.82it/s]
2685995it [00:01, 1700026.20it/s]
2857303it [00:01, 1703921.06it/s]
3027698it [00:01, 1698919.28it/s]
3197595it [00:01, 1693076.16it/s]
3366910it [00:02, 1673006.85it/s]
3537210it [00:02, 1681760.06it/s]
3705432it [00:02, 1677843.38it/s]
3873850it [00:02, 1679706.47it/s]
4042749it [00:02, 1682356.15it/s]
4213321it [00:02, 1689315.94it/s]
4382268it [00:02, 1688667.33it/s]
4551477it [00:02, 1689663.60it/s]
4720451it [00:02, 1684236.42it/s]
4889483it [00:02, 1686031.99it/s]
5058707it [00:03, 1687865.32it/s]
5228703it [00:03, 1691465.40it/s]
5397854it [00:03, 1691108.33it/s]
5566968it [00:03, 1684645.44it/s]
5735440it [00:03, 1684442.47it/s]
5903890it [00:03, 1682353.50it/s]
6072129it [00:03, 1678656.04it/s]
6240247it [00:03, 1679387.22it/s]
6408189it [00:03, 1674545.01it/s]
6575648it [00:03, 1669602.21it/s]
6742613it [00:04, 1664442.18it/s]
6910082it [00:04, 1667475.42it/s]
7078626it [00:04, 1672819.69it/s]
7246345it [00:04, 1673983.26it/s]
7415919it [00:04, 1680472.91it/s]
7584829it [00:04, 1683030.32it/s]
7753634it [00:04, 1684505.16it/s]
7922672it [00:04, 1686234.33it/s]
8092943it [00:04, 1691140.00it/s]
8262059it [00:04, 1688949.87it/s]
8430956it [00:05, 1687479.55it/s]
8599706it [00:05, 1685018.98it/s]
8768210it [00:05, 1683483.99it/s]
8936560it [00:05, 1676903.65it/s]
9105309it [00:05, 1680029.67it/s]
9274711it [00:05, 1684187.26it/s]
9443364it [00:05, 1684860.25it/s]
9613935it [00:05, 1691081.13it/s]
9784500it [00:05, 1695419.89it/s]
9954575it [00:05, 1696936.97it/s]
10124271it [00:06, 1695077.05it/s]
10293781it [00:06, 1694338.75it/s]
10463217it [00:06, 1684267.65it/s]
10631774it [00:06, 1684632.92it/s]
10801392it [00:06, 1688057.80it/s]
10970206it [00:06, 1686230.06it/s]
11138835it [00:06, 1673065.28it/s]
11306265it [00:06, 1673403.79it/s]
11474091it [00:06, 1674821.55it/s]
11643319it [00:06, 1679927.11it/s]
11811323it [00:07, 1675935.57it/s]
11980872it [00:07, 1681750.89it/s]
12149056it [00:07, 1680576.53it/s]
12318453it [00:07, 1684523.66it/s]
12489373it [00:07, 1691881.57it/s]
12658566it [00:07, 1686838.45it/s]
12827256it [00:07, 1684030.07it/s]
12995664it [00:07, 1682957.16it/s]
13139385it [00:07, 1681728.99it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
tabix -s 1 -b 2 -e 2 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz
seqtool depth_hist -nbins 500 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv
cat 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.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 2 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.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 2 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.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 2 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.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: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai
cat 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bKP-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt
+ merge_qc -folders 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
+ head -n1 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv