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/72/948528d223c9886f4e85871c70d5ec/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/819bbd1d063640fe52aea8e00d779a/aih-tih-sc-75c3a9-R1_B23WHYVLT4_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/72/948528d223c9886f4e85871c70d5ec/.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-rnd-pltf-dev-nextflow-scratch-01/work/f6/819bbd1d063640fe52aea8e00d779a/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
==> STAGING COMPLETE (11 inputs)
+ mkdir aih-tih-sc-75c3a9-R1_B23WHYVLT4_1
+ all_qc -bam aih-tih-sc-75c3a9-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-75c3a9-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20
mkdir -p aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-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-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/full_bed.bed
seqtool depth -bam aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.depth.gz
saturation_plot -bams aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/saturation_qc.tsv
fragment_size -bams aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-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-75c3a9-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-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-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-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-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
0it [00:00, ?it/s]
153367it [00:00, 1533601.99it/s]
315464it [00:00, 1584963.77it/s]
486491it [00:00, 1642159.33it/s]
658721it [00:00, 1673588.46it/s]
830601it [00:00, 1689870.80it/s]
999703it [00:00, 1690244.24it/s]
1172188it [00:00, 1701533.74it/s]
1346945it [00:00, 1716145.06it/s]
1520614it [00:00, 1722552.51it/s]
1693420it [00:01, 1724238.00it/s]
1865844it [00:01, 1715142.18it/s]
2040594it [00:01, 1724767.89it/s]
2215365it [00:01, 1731682.44it/s]
2388543it [00:01, 1727589.61it/s]
2566039it [00:01, 1741814.21it/s]
2740231it [00:01, 1736187.91it/s]
2913860it [00:01, 1728674.91it/s]
3086740it [00:01, 1716988.96it/s]
3260773it [00:01, 1723924.07it/s]
3433186it [00:02, 1699907.98it/s]
3603727it [00:02, 1701487.52it/s]
3778187it [00:02, 1714282.76it/s]
3950033it [00:02, 1715514.63it/s]
4122826it [00:02, 1719205.09it/s]
4294775it [00:02, 1691771.02it/s]
4465573it [00:02, 1696553.91it/s]
4635312it [00:02, 1687556.62it/s]
4804129it [00:02, 1677495.66it/s]
4977556it [00:02, 1694300.74it/s]
5150434it [00:03, 1704535.12it/s]
5326334it [00:03, 1720751.89it/s]
5499030it [00:03, 1722526.31it/s]
5672078it [00:03, 1724692.05it/s]
5844569it [00:03, 1721428.05it/s]
6018963it [00:03, 1728126.13it/s]
6191789it [00:03, 1723486.71it/s]
6364149it [00:03, 1709068.39it/s]
6535087it [00:03, 1698612.98it/s]
6706289it [00:03, 1702564.99it/s]
6876570it [00:04, 1701727.20it/s]
7046759it [00:04, 1685449.35it/s]
7217065it [00:04, 1690663.40it/s]
7388917it [00:04, 1698896.71it/s]
7558836it [00:04, 1698895.27it/s]
7728746it [00:04, 1695225.22it/s]
7898284it [00:04, 1691563.17it/s]
8067451it [00:04, 1688209.02it/s]
8237882it [00:04, 1693002.44it/s]
8407884it [00:04, 1695085.84it/s]
8579826it [00:05, 1702216.12it/s]
8750227it [00:05, 1702738.09it/s]
8921361it [00:05, 1705260.17it/s]
9091891it [00:05, 1694039.92it/s]
9261314it [00:05, 1692015.51it/s]
9434095it [00:05, 1702692.70it/s]
9605362it [00:05, 1705662.33it/s]
9779764it [00:05, 1717128.66it/s]
9953756it [00:05, 1723941.11it/s]
10128579it [00:05, 1731152.24it/s]
10301701it [00:06, 1726970.45it/s]
10474405it [00:06, 1721963.25it/s]
10646609it [00:06, 1706911.10it/s]
10817330it [00:06, 1705105.96it/s]
10987861it [00:06, 1696115.32it/s]
11157492it [00:06, 1682959.42it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
11325814it [00:06, 1682214.07it/s]
11494053it [00:06, 1678017.98it/s]
11661866it [00:06, 1665457.37it/s]
11828432it [00:06, 1663366.22it/s]
11996509it [00:07, 1668531.22it/s]
12167317it [00:07, 1680258.65it/s]
12335359it [00:07, 1680088.34it/s]
12505378it [00:07, 1685931.75it/s]
12673981it [00:07, 1683532.11it/s]
12843827it [00:07, 1687937.03it/s]
13012627it [00:07, 1686118.10it/s]
13092638it [00:07, 1700811.08it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
tabix -s 1 -b 2 -e 2 aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.depth.gz
seqtool depth_hist -nbins 500 aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.depth_hist.tsv
cat aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md -output aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/aih-tih-sc-75c3a9-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-75c3a9-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-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-75c3a9-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-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-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-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-75c3a9-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-75c3a9-R1_B23WHYVLT4_1/aih-tih-sc-75c3a9-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-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.md.bai