Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/b2b41b68398ceec482172096b4b95d/659_bNS-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.fa
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/b1693f0f6611bb071a2d338c79cdb7/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/b2b41b68398ceec482172096b4b95d/659_bNS-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.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/a9/b1693f0f6611bb071a2d338c79cdb7/.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_bNS-T1-TRNA-1_B23MHV2LT4_1
+ all_qc -bam 659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20
mkdir -p 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed
seqtool depth -bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz
saturation_plot -bams 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv
fragment_size -bams 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
0it [00:00, ?it/s]
132448it [00:00, 1324386.54it/s]
292701it [00:00, 1487881.65it/s]
459607it [00:00, 1570569.81it/s]
616665it [00:00, 1568865.97it/s]
773552it [00:00, 1561127.83it/s]
932165it [00:00, 1569541.52it/s]
1095042it [00:00, 1588822.58it/s]
1253934it [00:00, 1555704.56it/s]
1423639it [00:00, 1599167.12it/s]
1591326it [00:01, 1622862.21it/s]
1753754it [00:01, 1486581.95it/s]
1921037it [00:01, 1539432.97it/s]
2090391it [00:01, 1583922.45it/s]
2265110it [00:01, 1631590.82it/s]
2438755it [00:01, 1662439.68it/s]
2610215it [00:01, 1677855.28it/s]
2778684it [00:01, 1548312.33it/s]
2935890it [00:01, 1514141.61it/s]
3099428it [00:01, 1548102.73it/s]
3271037it [00:02, 1596225.93it/s]
3431861it [00:02, 1592404.34it/s]
3591934it [00:02, 1556121.85it/s]
3748239it [00:02, 1467635.90it/s]
3896309it [00:02, 1383957.17it/s]
4036215it [00:02, 1316239.48it/s]
4202308it [00:02, 1409389.33it/s]
4369412it [00:02, 1482222.43it/s]
4521151it [00:02, 1492206.64it/s]
4677128it [00:03, 1511713.13it/s]
4833286it [00:03, 1526258.25it/s]
4989126it [00:03, 1535573.58it/s]
5143240it [00:03, 1533954.78it/s]
5297024it [00:03, 1424542.49it/s]
5466996it [00:03, 1502228.03it/s]
5637770it [00:03, 1561169.43it/s]
5809055it [00:03, 1605284.75it/s]
5977737it [00:03, 1629201.50it/s]
6144205it [00:03, 1637149.95it/s]
6309322it [00:04, 1641251.27it/s]
6473881it [00:04, 1638505.57it/s]
6639743it [00:04, 1644365.00it/s]
6804396it [00:04, 1643701.72it/s]
6968918it [00:04, 1613799.06it/s]
7140561it [00:04, 1644069.11it/s]
7312113it [00:04, 1665233.65it/s]
7480734it [00:04, 1671451.25it/s]
7654156it [00:04, 1690057.62it/s]
7825454it [00:04, 1696879.91it/s]
7995211it [00:05, 1674309.14it/s]
8162753it [00:05, 1660813.98it/s]
8330982it [00:05, 1667092.23it/s]
8497762it [00:05, 1650058.93it/s]
8664406it [00:05, 1654873.21it/s]
8829952it [00:05, 1532797.09it/s]
9002290it [00:05, 1586533.99it/s]
9178075it [00:05, 1635608.79it/s]
9352791it [00:05, 1668030.92it/s]
9526572it [00:06, 1688485.38it/s]
9700565it [00:06, 1703658.25it/s]
9873047it [00:06, 1709894.04it/s]
10044432it [00:06, 1694937.74it/s]
10214224it [00:06, 1695057.95it/s]
10383939it [00:06, 1693658.23it/s]
10553816it [00:06, 1695042.02it/s]
10723423it [00:06, 1690322.81it/s]
10892529it [00:06, 1687603.38it/s]
11062790it [00:06, 1692015.59it/s]
11234283it [00:07, 1698816.13it/s]
11406486it [00:07, 1705735.17it/s]
11577601it [00:07, 1707332.83it/s]
11751308it [00:07, 1716101.03it/s]
11922930it [00:07, 1703756.65it/s]
12093334it [00:07, 1655898.38it/s]
12229420it [00:07, 1604664.37it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
tabix -s 1 -b 2 -e 2 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz
seqtool depth_hist -nbins 500 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv
cat 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/read_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/depth_stats.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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/reads_per_target.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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai
cat 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt
+ merge_qc -folders 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
+ head -n1 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv