Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/67ec575eab1b85319d951586af5c3e/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_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/3c/0bb5aa371672e6a7bf55c63c76772a/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/67ec575eab1b85319d951586af5c3e/aih-tih-sc-4f4d6e-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/3c/0bb5aa371672e6a7bf55c63c76772a/.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-4f4d6e-R1_B23WHYVLT4_1
+ all_qc -bam aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20
mkdir -p aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/full_bed.bed
saturation_plot -bams aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1
seqtool depth -bam aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth.gz
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/saturation_qc.tsv
fragment_size -bams aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bai
0it [00:00, ?it/s]
121358it [00:00, 1213101.04it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
246414it [00:00, 1235101.66it/s]
382958it [00:00, 1294583.21it/s]
517556it [00:00, 1314845.84it/s]
649042it [00:00, 1303104.12it/s]
779506it [00:00, 1303600.52it/s]
909879it [00:00, 1301213.69it/s]
1040009it [00:00, 1263481.73it/s]
1166571it [00:00, 1235272.16it/s]
1290322it [00:01, 1213419.94it/s]
1411840it [00:01, 1206323.12it/s]
1535895it [00:01, 1216415.76it/s]
1657641it [00:01, 1211074.91it/s]
1785342it [00:01, 1230625.59it/s]
1919160it [00:01, 1262626.78it/s]
2051013it [00:01, 1279290.15it/s]
2180834it [00:01, 1284926.10it/s]
2314610it [00:01, 1300715.62it/s]
2445097it [00:01, 1301777.85it/s]
2577087it [00:02, 1307187.70it/s]
2711532it [00:02, 1318204.12it/s]
2843372it [00:02, 1317866.68it/s]
2978149it [00:02, 1326732.72it/s]
3112761it [00:02, 1332528.79it/s]
3246022it [00:02, 1290519.39it/s]
3375901it [00:02, 1292920.51it/s]
3505403it [00:02, 1279338.28it/s]
3633497it [00:02, 1234893.92it/s]
3757365it [00:02, 1192175.34it/s]
3877036it [00:03, 1138663.64it/s]
3991513it [00:03, 1104063.19it/s]
4102374it [00:03, 1075627.72it/s]
4210238it [00:03, 1060160.51it/s]
4327688it [00:03, 1092377.43it/s]
4458247it [00:03, 1153596.39it/s]
4574099it [00:03, 1118026.95it/s]
4686402it [00:03, 1094157.91it/s]
4813844it [00:03, 1145661.61it/s]
4946010it [00:04, 1196685.65it/s]
5071892it [00:04, 1214865.61it/s]
5195974it [00:04, 1222492.54it/s]
5318528it [00:04, 1215247.19it/s]
5441469it [00:04, 1219412.57it/s]
5563567it [00:04, 1203488.04it/s]
5684061it [00:04, 1162741.96it/s]
5802892it [00:04, 1169998.85it/s]
5923018it [00:04, 1179121.58it/s]
6044186it [00:04, 1188693.40it/s]
6166183it [00:05, 1197855.52it/s]
6291423it [00:05, 1213971.59it/s]
6413186it [00:05, 1215041.91it/s]
6537672it [00:05, 1223926.81it/s]
6660120it [00:05, 1219439.75it/s]
6787631it [00:05, 1236037.89it/s]
6911272it [00:05, 1219324.89it/s]
7036487it [00:05, 1228999.73it/s]
7159449it [00:05, 1223759.10it/s]
7284804it [00:05, 1232593.70it/s]
7418401it [00:06, 1263293.35it/s]
7544777it [00:06, 1250519.32it/s]
7673843it [00:06, 1262408.17it/s]
7800136it [00:06, 1252039.63it/s]
7936119it [00:06, 1283995.67it/s]
8064829it [00:06, 1229635.11it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
tabix -s 1 -b 2 -e 2 aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth.gz
seqtool depth_hist -nbins 500 aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth_hist.tsv
cat aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md -output aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai
cat aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/qc_complete.txt
+ merge_qc -folders aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md -output aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1_full_basic_stats.tsv