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/0d/72ab2090fba893a22056e0e113e8e6/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.dict
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/f61f95c52687d9bb8871e2fef76f86/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bam
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/0d/72ab2090fba893a22056e0e113e8e6/.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/28/f61f95c52687d9bb8871e2fef76f86/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
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 aih-tih-sc-c55577-R1_B23WHYVLT4_1
+ all_qc -bam aih-tih-sc-c55577-R1_B23WHYVLT4_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 aih-tih-sc-c55577-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20
mkdir -p aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/full_bed.bed
saturation_plot -bams aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1
seqtool depth -bam aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.depth.gz
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/saturation_qc.tsv
fragment_size -bams aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_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: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
0it [00:00, ?it/s]
147534it [00:00, 1475214.79it/s]
307568it [00:00, 1548764.02it/s]
462445it [00:00, 1533890.83it/s]
629400it [00:00, 1587098.79it/s]
802131it [00:00, 1637436.40it/s]
972771it [00:00, 1660725.21it/s]
1145661it [00:00, 1682858.66it/s]
1313975it [00:00, 1673580.46it/s]
1488161it [00:00, 1694800.03it/s]
1662847it [00:01, 1710795.25it/s]
1836744it [00:01, 1719374.12it/s]
2008702it [00:01, 1705057.74it/s]
2181029it [00:01, 1710432.76it/s]
2352103it [00:01, 1674669.43it/s]
2531714it [00:01, 1710584.22it/s]
2712766it [00:01, 1740250.83it/s]
2889872it [00:01, 1749396.50it/s]
3064938it [00:01, 1654000.53it/s]
3239184it [00:01, 1679316.41it/s]
3408015it [00:02, 1671881.39it/s]
3580921it [00:02, 1688575.85it/s]
3750254it [00:02, 1648596.07it/s]
3927039it [00:02, 1683289.20it/s]
4095814it [00:02, 1651762.77it/s]
4269876it [00:02, 1677641.50it/s]
4437988it [00:02, 1570599.17it/s]
4596534it [00:02, 1559262.49it/s]
4765426it [00:02, 1596126.83it/s]
4937141it [00:02, 1631105.79it/s]
5110383it [00:03, 1660686.66it/s]
5280153it [00:03, 1671558.80it/s]
5447748it [00:03, 1650381.44it/s]
5613134it [00:03, 1630481.68it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
5787482it [00:03, 1663602.98it/s]
5961349it [00:03, 1685718.07it/s]
6130137it [00:03, 1666887.17it/s]
6297007it [00:03, 1626289.00it/s]
6466959it [00:03, 1647592.08it/s]
6631985it [00:04, 1640479.22it/s]
6796213it [00:04, 1598842.95it/s]
6968722it [00:04, 1635547.34it/s]
7141548it [00:04, 1662731.13it/s]
7315410it [00:04, 1685113.61it/s]
7485001it [00:04, 1688280.40it/s]
7658899it [00:04, 1703345.71it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
7835977it [00:04, 1723364.77it/s]
8010353it [00:04, 1729427.76it/s]
8186893it [00:04, 1740159.34it/s]
8363034it [00:05, 1746490.82it/s]
8537722it [00:05, 1739277.76it/s]
8713122it [00:05, 1743646.84it/s]
8887512it [00:05, 1730949.99it/s]
9062557it [00:05, 1736734.66it/s]
9237535it [00:05, 1740527.83it/s]
9411610it [00:05, 1691014.89it/s]
9584176it [00:05, 1701143.71it/s]
9758532it [00:05, 1713634.22it/s]
9932373it [00:05, 1720953.81it/s]
10108644it [00:06, 1733350.53it/s]
10285461it [00:06, 1743705.53it/s]
10460807it [00:06, 1746520.17it/s]
10637239it [00:06, 1751812.09it/s]
10812463it [00:06, 1727987.87it/s]
10986643it [00:06, 1732051.01it/s]
11007108it [00:06, 1683002.88it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
tabix -s 1 -b 2 -e 2 aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.depth.gz
seqtool depth_hist -nbins 500 aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.depth_hist.tsv
cat aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-c55577-R1_B23WHYVLT4_1.md -output aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/aih-tih-sc-c55577-R1_B23WHYVLT4_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 aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_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 aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_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 aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_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: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c55577-R1_B23WHYVLT4_1.md.bai
cat aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "aih-tih-sc-c55577-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md/qc_complete.txt
+ merge_qc -folders aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1.md -output aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-c55577-R1_B23WHYVLT4_1/aih-tih-sc-c55577-R1_B23WHYVLT4_1_full_basic_stats.tsv