Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/6bb5aecdcc067e7de32f72b99b2fff/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_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/d2/76889aa8c4b2c1600ceeddb0102541/.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/d2/76889aa8c4b2c1600ceeddb0102541/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/6bb5aecdcc067e7de32f72b99b2fff/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.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 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1
+ all_qc -bam 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_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 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1 -reference ref_genome.fa -region chr20
mkdir -p 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed
seqtool depth -bam 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -bed 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz
saturation_plot -bams 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -region chr20 -output 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_qc.tsv
fragment_size -bams 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -region chr20 -output_prefix 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup && contamination -input 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_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: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
0it [00:00, ?it/s]
148998it [00:00, 1489612.06it/s]
302361it [00:00, 1515460.68it/s]
453908it [00:00, 1236666.12it/s]
614722it [00:00, 1365548.80it/s]
777897it [00:00, 1453739.35it/s]
941647it [00:00, 1512793.95it/s]
1099779it [00:00, 1534339.94it/s]
1262022it [00:00, 1561643.13it/s]
1423140it [00:00, 1576839.85it/s]
1583592it [00:01, 1585262.16it/s]
1745108it [00:01, 1594317.39it/s]
1906077it [00:01, 1598902.64it/s]
2069447it [00:01, 1609239.86it/s]
2238418it [00:01, 1633455.80it/s]
2403395it [00:01, 1638348.10it/s]
2567359it [00:01, 1634582.31it/s]
2730909it [00:01, 1626830.77it/s]
2893663it [00:01, 1620604.29it/s]
3055776it [00:01, 1603473.57it/s]
3216191it [00:02, 1597570.43it/s]
3375994it [00:02, 1587216.06it/s]
3538121it [00:02, 1597293.04it/s]
3701791it [00:02, 1608974.65it/s]
3862726it [00:02, 1551297.60it/s]
4018299it [00:02, 1494321.92it/s]
4172078it [00:02, 1506724.03it/s]
4336240it [00:02, 1545817.26it/s]
4491308it [00:02, 1530926.51it/s]
4644743it [00:03, 1458764.99it/s]
4794513it [00:03, 1469834.97it/s]
4942425it [00:03, 1472418.31it/s]
5090123it [00:03, 1473524.37it/s]
5240431it [00:03, 1482206.32it/s]
5388893it [00:03, 1474156.56it/s]
5536479it [00:03, 1452327.06it/s]
5684646it [00:03, 1460923.50it/s]
5831475it [00:03, 1463076.22it/s]
5983000it [00:03, 1478547.97it/s]
6130938it [00:04, 1461985.41it/s]
6297283it [00:04, 1521625.61it/s]
6453891it [00:04, 1534819.38it/s]
6614843it [00:04, 1557053.78it/s]
6780611it [00:04, 1587090.60it/s]
6944840it [00:04, 1603578.45it/s]
7106245it [00:04, 1606692.81it/s]
7268766it [00:04, 1612220.24it/s]
7432316it [00:04, 1619177.31it/s]
7594256it [00:04, 1618052.26it/s]
7756077it [00:05, 1388237.34it/s]
7900621it [00:05, 1244160.77it/s]
8062166it [00:05, 1338388.71it/s]
8219891it [00:05, 1401814.60it/s]
8373122it [00:05, 1437738.77it/s]
8530017it [00:05, 1474769.35it/s]
8686524it [00:05, 1500710.39it/s]
8845247it [00:05, 1525881.73it/s]
9007507it [00:05, 1554272.24it/s]
9164855it [00:06, 1559809.07it/s]
9323185it [00:06, 1566767.52it/s]
9486715it [00:06, 1587160.72it/s]
9650605it [00:06, 1602587.94it/s]
9814803it [00:06, 1614347.03it/s]
9978707it [00:06, 1621720.30it/s]
10141129it [00:06, 1622445.00it/s]
10303482it [00:06, 1607785.78it/s]
10466213it [00:06, 1613584.33it/s]
10627650it [00:06, 1610521.15it/s]
10788757it [00:07, 1604027.12it/s]
10949201it [00:07, 1597057.18it/s]
11111914it [00:07, 1605996.06it/s]
11274368it [00:07, 1611513.93it/s]
11438684it [00:07, 1620955.27it/s]
11597774it [00:07, 1540848.20it/s]
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
tabix -s 1 -b 2 -e 2 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz
seqtool depth_hist -nbins 500 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz > 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv
cat 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_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 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_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 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz> 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_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 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_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: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
cat 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md/qc_complete.txt
+ merge_qc -folders 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv
+ head -n1 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv