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/d0/62cdf2be78e859c0949bdcb7e55fb1/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/1339e7516c2a3cfa83cbaa63ed2dcd/aih-tih-sc-184b05-R1_A23YTGFLT4_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/31/1339e7516c2a3cfa83cbaa63ed2dcd/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/62cdf2be78e859c0949bdcb7e55fb1/.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-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
==> STAGING COMPLETE (11 inputs)
+ mkdir aih-tih-sc-184b05-R1_A23YTGFLT4_1
+ all_qc -bam aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20
mkdir -p aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/full_bed.bed
seqtool depth -bam aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.depth.gz
saturation_plot -bams aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/saturation_qc.tsv
fragment_size -bams aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
0it [00:00, ?it/s]
67924it [00:00, 679119.21it/s]
135836it [00:00, 655089.45it/s]
201403it [00:00, 649984.77it/s]
266428it [00:00, 645746.81it/s]
331016it [00:00, 642093.42it/s]
395233it [00:00, 641527.46it/s]
459390it [00:00, 639788.24it/s]
523371it [00:00, 637747.71it/s]
587248it [00:00, 638042.24it/s]
652432it [00:01, 642257.19it/s]
732492it [00:01, 690496.84it/s]
809100it [00:01, 713396.02it/s]
880461it [00:01, 707156.51it/s]
961694it [00:01, 738657.09it/s]
1052345it [00:01, 788957.18it/s]
1132562it [00:01, 792887.82it/s]
1211892it [00:01, 755312.39it/s]
1292683it [00:01, 770531.17it/s]
1370069it [00:01, 767416.51it/s]
1447613it [00:02, 769662.49it/s]
1524744it [00:02, 753854.06it/s]
1604788it [00:02, 767448.64it/s]
1689398it [00:02, 790599.65it/s]
1774343it [00:02, 808009.67it/s]
1859625it [00:02, 821302.58it/s]
1942070it [00:02, 822126.05it/s]
2024354it [00:02, 786412.73it/s]
2103363it [00:02, 741471.46it/s]
2178192it [00:02, 713865.48it/s]
2250137it [00:03, 694957.76it/s]
2320014it [00:03, 686626.57it/s]
2388909it [00:03, 677178.95it/s]
2456765it [00:03, 672870.51it/s]
2526876it [00:03, 680924.43it/s]
2602123it [00:03, 701709.95it/s]
2672424it [00:03, 683942.90it/s]
2740976it [00:03, 675650.83it/s]
2808649it [00:03, 671605.66it/s]
2875879it [00:04, 668613.77it/s]
2942784it [00:04, 666776.62it/s]
3010439it [00:04, 669631.22it/s]
3077427it [00:04, 669674.83it/s]
3144412it [00:04, 667606.97it/s]
3212307it [00:04, 670960.75it/s]
3279415it [00:04, 670307.85it/s]
3346454it [00:04, 661609.62it/s]
3412642it [00:04, 661660.93it/s]
3478827it [00:04, 658432.17it/s]
3544685it [00:05, 654632.25it/s]
3610178it [00:05, 654699.48it/s]
3675706it [00:05, 654852.97it/s]
3741198it [00:05, 654054.24it/s]
3806767it [00:05, 654434.78it/s]
3872777it [00:05, 656108.21it/s]
3938391it [00:05, 646952.69it/s]
4003115it [00:05, 644341.07it/s]
4067834it [00:05, 645162.36it/s]
4133081it [00:05, 647315.37it/s]
4197965it [00:06, 647747.41it/s]
4262749it [00:06, 646159.75it/s]
4327702it [00:06, 647148.09it/s]
4393598it [00:06, 650561.08it/s]
4459498it [00:06, 653066.09it/s]
4526290it [00:06, 657497.73it/s]
4593037it [00:06, 660462.97it/s]
4660356it [00:06, 664256.68it/s]
4726784it [00:06, 661879.32it/s]
4793034it [00:06, 662042.50it/s]
4859241it [00:07, 660112.09it/s]
4926641it [00:07, 664245.08it/s]
4993069it [00:07, 663322.91it/s]
5059404it [00:07, 661003.87it/s]
5125508it [00:07, 659857.47it/s]
5191496it [00:07, 655639.03it/s]
5257066it [00:07, 653731.87it/s]
5325115it [00:07, 661679.28it/s]
5401982it [00:07, 693495.59it/s]
5478721it [00:07, 715547.41it/s]
5561985it [00:08, 750556.88it/s]
5641086it [00:08, 762649.59it/s]
5717371it [00:08, 757216.11it/s]
5799400it [00:08, 775999.91it/s]
5885113it [00:08, 800213.70it/s]
5966456it [00:08, 804040.88it/s]
6046882it [00:08, 775827.17it/s]
6124689it [00:08, 770959.61it/s]
6201937it [00:08, 769361.75it/s]
6286463it [00:08, 791613.61it/s]
6378130it [00:09, 828622.85it/s]
6480720it [00:09, 887237.88it/s]
6571103it [00:09, 892160.08it/s]
6661258it [00:09, 894937.06it/s]
6754565it [00:09, 906320.36it/s]
6845253it [00:09, 827387.81it/s]
6929355it [00:09, 767821.12it/s]
7010670it [00:09, 780049.62it/s]
7090587it [00:09, 785356.49it/s]
7182988it [00:10, 824807.05it/s]
7274155it [00:10, 849886.88it/s]
7367087it [00:10, 873075.52it/s]
7454939it [00:10, 864869.43it/s]
7541814it [00:10, 838453.43it/s]
7626067it [00:10, 817499.82it/s]
7708155it [00:10, 801865.29it/s]
7788584it [00:10, 793350.51it/s]
7871323it [00:10, 803074.34it/s]
7951779it [00:10, 783485.81it/s]
8030289it [00:11, 772390.24it/s]
8126606it [00:11, 827489.54it/s]
8216146it [00:11, 847302.03it/s]
8314028it [00:11, 886008.48it/s]
8409528it [00:11, 906412.09it/s]
8503362it [00:11, 915798.07it/s]
8595092it [00:11, 816659.90it/s]
8678832it [00:11, 761467.63it/s]
8756914it [00:11, 721958.41it/s]
8830586it [00:12, 702839.98it/s]
8906867it [00:12, 718867.90it/s]
8987535it [00:12, 743129.38it/s]
9068702it [00:12, 762493.10it/s]
9151269it [00:12, 780662.57it/s]
9235705it [00:12, 799190.27it/s]
9323389it [00:12, 821994.05it/s]
9405943it [00:12, 754408.47it/s]
9482671it [00:12, 721836.11it/s]
9555897it [00:13, 693789.65it/s]
9638053it [00:13, 728713.33it/s]
9724541it [00:13, 766945.19it/s]
9813156it [00:13, 801056.03it/s]
9901464it [00:13, 824848.11it/s]
9984573it [00:13, 757417.37it/s]
10061754it [00:13, 709978.64it/s]
10134140it [00:13, 691336.60it/s]
10204199it [00:13, 681400.28it/s]
10272934it [00:14, 682397.53it/s]
10348092it [00:14, 701926.90it/s]
10436112it [00:14, 753163.94it/s]
10512285it [00:14, 755629.89it/s]
10588214it [00:14, 724707.85it/s]
10661167it [00:14, 699767.07it/s]
10731582it [00:14, 678224.74it/s]
10799756it [00:14, 671270.61it/s]
10867104it [00:14, 669646.46it/s]
10934216it [00:14, 665672.22it/s]
11000877it [00:15, 657600.18it/s]
11082350it [00:15, 703217.65it/s]
11169255it [00:15, 751794.94it/s]
11264193it [00:15, 810104.50it/s]
11358872it [00:15, 850628.32it/s]
11446882it [00:15, 859347.83it/s]
11532987it [00:15, 833591.43it/s]
11624792it [00:15, 858255.85it/s]
11718099it [00:15, 880276.61it/s]
11806348it [00:16, 835055.59it/s]
11890455it [00:16, 770478.31it/s]
11968731it [00:16, 735114.32it/s]
12043215it [00:16, 712951.48it/s]
12115156it [00:16, 699062.67it/s]
12185456it [00:16, 691035.64it/s]
12254793it [00:16, 685106.37it/s]
12323439it [00:16, 677841.19it/s]
12391297it [00:16, 672283.28it/s]
12458562it [00:17, 665739.44it/s]
12525152it [00:17, 656894.56it/s]
12590850it [00:17, 653942.95it/s]
12656244it [00:17, 652585.99it/s]
12721499it [00:17, 650525.89it/s]
12792894it [00:17, 669218.46it/s]
12859844it [00:17, 663346.30it/s]
12926204it [00:17, 656938.01it/s]
12999299it [00:17, 678725.28it/s]
13092743it [00:17, 754496.64it/s]
13177405it [00:18, 781872.01it/s]
13258720it [00:18, 791170.62it/s]
13337922it [00:18, 789769.66it/s]
13425535it [00:18, 815534.94it/s]
13507685it [00:18, 817290.57it/s]
13597967it [00:18, 842752.98it/s]
13682274it [00:18, 815947.54it/s]
13764073it [00:18, 761195.26it/s]
13840991it [00:18, 725905.15it/s]
13914319it [00:18, 705902.24it/s]
13985412it [00:19, 688757.22it/s]
14054614it [00:19, 677334.82it/s]
14122539it [00:19, 671087.58it/s]
14189756it [00:19, 667773.19it/s]
14260809it [00:19, 680049.18it/s]
14336393it [00:19, 702090.98it/s]
14414704it [00:19, 725866.50it/s]
14487435it [00:19, 704312.02it/s]
14558083it [00:19, 686674.57it/s]
14645894it [00:20, 741761.95it/s]
14721451it [00:20, 745765.77it/s]
14801827it [00:20, 762788.73it/s]
14879653it [00:20, 767341.91it/s]
14965182it [00:20, 793437.18it/s]
15044668it [00:20, 786972.21it/s]
15133910it [00:20, 818233.85it/s]
15147736it [00:20, 733572.52it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
tabix -s 1 -b 2 -e 2 aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.depth.gz
seqtool depth_hist -nbins 500 aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.depth_hist.tsv
cat aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-184b05-R1_A23YTGFLT4_1.md -output aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-184b05-R1_A23YTGFLT4_1.md.bai
cat aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md/qc_complete.txt
+ merge_qc -folders aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1.md -output aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-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-184b05-R1_A23YTGFLT4_1/aih-tih-sc-184b05-R1_A23YTGFLT4_1_full_basic_stats.tsv