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/25/1baee662d8cf5d4e2bdfcd3c9f9d00/.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/30/56aea1795c385bfe838ce8a8900a7c/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
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/25/1baee662d8cf5d4e2bdfcd3c9f9d00/.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/30/56aea1795c385bfe838ce8a8900a7c/aih-tih-sc-28eb14-R1_A23YTGFLT4_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 aih-tih-sc-28eb14-R1_A23YTGFLT4_1
+ all_qc -bam aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20
mkdir -p aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/full_bed.bed
seqtool depth -bam aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth.gz
saturation_plot -bams aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/saturation_qc.tsv
fragment_size -bams aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
0it [00:00, ?it/s]
140606it [00:00, 1405933.96it/s]
285982it [00:00, 1434002.34it/s]
442285it [00:00, 1492871.62it/s]
603023it [00:00, 1538039.16it/s]
766022it [00:00, 1571104.53it/s]
931361it [00:00, 1599046.58it/s]
1098218it [00:00, 1621597.64it/s]
1263347it [00:00, 1631015.03it/s]
1429150it [00:00, 1639429.47it/s]
1596019it [00:01, 1648433.47it/s]
1760863it [00:01, 1647850.41it/s]
1925649it [00:01, 1638981.24it/s]
2090161it [00:01, 1640805.66it/s]
2255206it [00:01, 1643518.70it/s]
2420915it [00:01, 1647550.89it/s]
2594081it [00:01, 1672801.86it/s]
2762072it [00:01, 1674836.82it/s]
2929561it [00:01, 1670970.34it/s]
3096664it [00:01, 1655804.46it/s]
3262277it [00:02, 1633430.68it/s]
3429448it [00:02, 1644723.15it/s]
3593990it [00:02, 1614804.19it/s]
3755613it [00:02, 1553077.78it/s]
3913854it [00:02, 1561464.80it/s]
4072718it [00:02, 1569339.81it/s]
4229949it [00:02, 1442800.92it/s]
4376278it [00:02, 1379791.63it/s]
4517343it [00:02, 1388229.99it/s]
4671138it [00:02, 1430397.38it/s]
4834627it [00:03, 1488942.05it/s]
4984591it [00:03, 1473509.61it/s]
5132689it [00:03, 1468104.44it/s]
5280013it [00:03, 1448893.75it/s]
5431094it [00:03, 1466911.82it/s]
5583261it [00:03, 1482984.00it/s]
5747014it [00:03, 1528652.46it/s]
5917782it [00:03, 1581733.15it/s]
6083956it [00:03, 1605531.20it/s]
6247815it [00:03, 1615292.53it/s]
6414028it [00:04, 1629259.20it/s]
6582645it [00:04, 1646262.52it/s]
6751218it [00:04, 1657954.12it/s]
6917063it [00:04, 1651709.14it/s]
7082273it [00:04, 1620793.54it/s]
7247060it [00:04, 1628745.76it/s]
7414125it [00:04, 1641150.52it/s]
7581184it [00:04, 1649878.96it/s]
7749287it [00:04, 1659139.34it/s]
7915296it [00:04, 1659337.61it/s]
8082168it [00:05, 1662116.64it/s]
8248409it [00:05, 1567006.83it/s]
8406238it [00:05, 1493023.93it/s]
8570306it [00:05, 1534450.86it/s]
8732736it [00:05, 1560137.06it/s]
8899808it [00:05, 1592206.72it/s]
9065502it [00:05, 1611149.95it/s]
9228537it [00:05, 1616794.18it/s]
9397590it [00:05, 1638637.14it/s]
9561775it [00:06, 1620781.57it/s]
9727364it [00:06, 1631141.79it/s]
9891435it [00:06, 1633797.61it/s]
10054954it [00:06, 1630241.91it/s]
10220586it [00:06, 1637873.02it/s]
10385977it [00:06, 1642633.15it/s]
10550294it [00:06, 1641098.83it/s]
10714441it [00:06, 1628500.99it/s]
10877336it [00:06, 1568922.19it/s]
11034693it [00:06, 1519358.44it/s]
11187170it [00:07, 1475903.11it/s]
11335248it [00:07, 1473627.80it/s]
11482941it [00:07, 1445995.31it/s]
11638274it [00:07, 1476860.62it/s]
11803413it [00:07, 1527678.11it/s]
11969649it [00:07, 1567222.34it/s]
12126711it [00:07, 1563612.33it/s]
12283307it [00:07, 1553247.68it/s]
12450791it [00:07, 1589102.94it/s]
12616595it [00:07, 1609560.73it/s]
12781668it [00:08, 1621805.97it/s]
12943953it [00:08, 1596800.93it/s]
13109710it [00:08, 1614743.58it/s]
13271315it [00:08, 1610923.02it/s]
13436760it [00:08, 1623835.85it/s]
13602345it [00:08, 1633349.32it/s]
13765738it [00:08, 1621573.85it/s]
13930532it [00:08, 1629346.50it/s]
14093512it [00:08, 1613716.11it/s]
14257034it [00:09, 1620066.91it/s]
14420396it [00:09, 1624000.87it/s]
14582833it [00:09, 1623506.28it/s]
14748544it [00:09, 1633515.72it/s]
14911918it [00:09, 1631842.14it/s]
15076682it [00:09, 1636543.31it/s]
15240349it [00:09, 1634785.64it/s]
15410865it [00:09, 1655763.88it/s]
15505077it [00:09, 1588817.71it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
tabix -s 1 -b 2 -e 2 aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth.gz
seqtool depth_hist -nbins 500 aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth_hist.tsv
cat aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md -output aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai
cat aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/qc_complete.txt
+ merge_qc -folders aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md -output aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_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-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1_full_basic_stats.tsv