Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/3195e5c3dbfb9ed2aaf4fb1b20a21d/659_6i-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-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/549d5710e3411f6f1c168b0e9fca9d/.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/d7/549d5710e3411f6f1c168b0e9fca9d/.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-rnd-pltf-dev-nextflow-scratch-01/work/89/3195e5c3dbfb9ed2aaf4fb1b20a21d/659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bam
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_6i-T1-TRNA-1_B23MHV2LT4_1
+ all_qc -bam 659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20
mkdir -p 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed
seqtool depth -bam 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/659_6i-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz
saturation_plot -bams 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv
fragment_size -bams 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: 659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
152431it [00:00, 1524209.70it/s]
319246it [00:00, 1608845.23it/s]
489537it [00:00, 1651660.14it/s]
660529it [00:00, 1674634.38it/s]
831288it [00:00, 1686496.64it/s]
1004116it [00:00, 1700679.53it/s]
1174502it [00:00, 1701699.90it/s]
1346680it [00:00, 1708072.01it/s]
1517627it [00:00, 1708489.17it/s]
1690275it [00:01, 1714022.20it/s]
1865233it [00:01, 1724881.00it/s]
2037722it [00:01, 1722953.59it/s]
2210018it [00:01, 1720248.40it/s]
2383981it [00:01, 1726072.29it/s]
2556590it [00:01, 1717916.98it/s]
2730270it [00:01, 1723495.31it/s]
2902857it [00:01, 1724123.98it/s]
3075276it [00:01, 1720164.62it/s]
3247299it [00:01, 1718955.12it/s]
3419199it [00:02, 1710648.44it/s]
3590759it [00:02, 1712112.80it/s]
3763201it [00:02, 1715777.40it/s]
3935864it [00:02, 1719010.19it/s]
4107771it [00:02, 1714253.24it/s]
4279203it [00:02, 1711792.23it/s]
4453015it [00:02, 1719648.82it/s]
4624986it [00:02, 1715332.86it/s]
4796525it [00:02, 1710203.12it/s]
4970418it [00:02, 1718768.81it/s]
5143381it [00:03, 1721937.71it/s]
5315582it [00:03, 1721464.73it/s]
5488917it [00:03, 1725009.78it/s]
5662116it [00:03, 1727074.62it/s]
5834827it [00:03, 1708344.66it/s]
6005709it [00:03, 1692602.75it/s]
6175147it [00:03, 1693093.98it/s]
6344495it [00:03, 1692426.83it/s]
6514857it [00:03, 1695737.30it/s]
6685597it [00:03, 1699195.48it/s]
6855533it [00:04, 1692504.25it/s]
7026192it [00:04, 1696686.43it/s]
7197777it [00:04, 1702299.35it/s]
7369973it [00:04, 1708164.98it/s]
7541033it [00:04, 1708765.36it/s]
7715992it [00:04, 1720979.04it/s]
7890609it [00:04, 1728465.73it/s]
8063461it [00:04, 1722885.38it/s]
8235757it [00:04, 1716629.09it/s]
8408900it [00:04, 1721029.19it/s]
8581785it [00:05, 1723348.91it/s]
8754127it [00:05, 1722636.72it/s][W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
8926396it [00:05, 1715890.95it/s]
9097994it [00:05, 1713328.11it/s]
9269333it [00:05, 1701487.46it/s]
9439500it [00:05, 1700544.01it/s]
9613661it [00:05, 1712770.66it/s]
9786748it [00:05, 1718020.02it/s]
9959330it [00:05, 1720332.90it/s]
10057456it [00:05, 1710235.66it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
tabix -s 1 -b 2 -e 2 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/659_6i-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz
seqtool depth_hist -nbins 500 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/659_6i-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/659_6i-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv
cat 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/659_6i-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_6i-T1-TRNA-1_B23MHV2LT4_1.md -output 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/659_6i-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23MHV2LT4_1.md.bai
cat 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt
+ merge_qc -folders 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1.md -output 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
+ head -n1 659_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-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_6i-T1-TRNA-1_B23MHV2LT4_1/659_6i-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv