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/42/eb95451e0a7738bc6a97c450bcb1ef/.command.sh
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/56/219f88f9b3096ab5a2db37d76646ba/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/eb95451e0a7738bc6a97c450bcb1ef/.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/56/219f88f9b3096ab5a2db37d76646ba/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
==> STAGING COMPLETE (11 inputs)
+ mkdir 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2
+ all_qc -bam 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2 -reference ref_genome.fa -region chr20
mkdir -p 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/full_bed.bed
seqtool depth -bam 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -bed 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz
saturation_plot -bams 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -region chr20 -output 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/saturation_qc.tsv
fragment_size -bams 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -region chr20 -output_prefix 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.mpileup && contamination -input 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.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: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
0it [00:00, ?it/s]
158098it [00:00, 1580826.98it/s]
324322it [00:00, 1628672.60it/s]
496354it [00:00, 1670310.84it/s]
667747it [00:00, 1687499.98it/s]
841472it [00:00, 1705413.08it/s]
1014563it [00:00, 1714055.70it/s]
1191084it [00:00, 1730754.68it/s]
1364860it [00:00, 1732961.60it/s]
1538696it [00:00, 1734623.81it/s]
1713885it [00:01, 1739931.51it/s]
1887879it [00:01, 1716114.43it/s]
2063797it [00:01, 1729065.46it/s]
2244476it [00:01, 1752429.50it/s]
2420470it [00:01, 1754661.45it/s]
2595979it [00:01, 1754501.66it/s]
2771459it [00:01, 1742534.83it/s]
2945750it [00:01, 1738594.36it/s]
3119635it [00:01, 1626576.63it/s]
3283723it [00:01, 1515029.60it/s]
3451718it [00:02, 1560277.17it/s]
3618018it [00:02, 1589195.89it/s]
3787487it [00:02, 1619450.31it/s]
3955409it [00:02, 1636809.04it/s]
4126349it [00:02, 1658088.22it/s]
4292845it [00:02, 1558368.18it/s]
4464202it [00:02, 1602339.56it/s]
4625819it [00:02, 1603411.56it/s]
4788877it [00:02, 1611289.26it/s]
4956925it [00:02, 1631591.08it/s]
5135141it [00:03, 1676083.52it/s]
5313716it [00:03, 1708612.97it/s]
5484917it [00:03, 1704110.15it/s]
5655566it [00:03, 1684085.36it/s]
5824183it [00:03, 1664359.42it/s]
5990794it [00:03, 1653895.29it/s]
6165858it [00:03, 1682268.54it/s]
6335770it [00:03, 1687247.31it/s]
6509579it [00:03, 1702167.04it/s]
6679878it [00:04, 1629010.93it/s]
6843470it [00:04, 1581292.99it/s]
7002255it [00:04, 1575057.77it/s]
7174475it [00:04, 1617492.56it/s]
7344089it [00:04, 1640449.91it/s]
7508519it [00:04, 1476350.12it/s]
7659368it [00:04, 1403247.85it/s]
7802282it [00:04, 1354537.93it/s]
7939535it [00:04, 1312863.68it/s][W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
8072019it [00:05, 1296741.58it/s]
8202432it [00:05, 1278855.72it/s]
8330760it [00:05, 1259201.31it/s]
8456935it [00:05, 1229427.34it/s]
8580712it [00:05, 1231766.64it/s]
8704028it [00:05, 1230452.60it/s]
8829643it [00:05, 1237908.55it/s]
8953522it [00:05, 1231615.35it/s]
9076740it [00:05, 1198948.63it/s]
9200772it [00:05, 1210945.34it/s]
9326745it [00:06, 1225206.56it/s]
9451559it [00:06, 1231948.83it/s]
9574868it [00:06, 1222592.22it/s]
9700736it [00:06, 1233251.54it/s]
9825764it [00:06, 1238288.68it/s]
9949650it [00:06, 1231641.32it/s]
10074174it [00:06, 1235664.72it/s][W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
10198733it [00:06, 1238578.21it/s]
10322617it [00:06, 1234511.88it/s]
10446088it [00:06, 1222034.89it/s]
10569445it [00:07, 1225401.95it/s]
10692015it [00:07, 1215341.17it/s]
10813582it [00:07, 1206709.65it/s]
10934281it [00:07, 1195631.06it/s]
11056301it [00:07, 1202870.99it/s]
11180316it [00:07, 1213915.96it/s]
11319998it [00:07, 1268294.03it/s]
11491765it [00:07, 1402359.87it/s]
11666804it [00:07, 1506244.15it/s]
11844117it [00:07, 1586069.40it/s]
12015350it [00:08, 1623854.44it/s]
12186431it [00:08, 1649816.71it/s]
12356094it [00:08, 1663761.73it/s]
12522514it [00:08, 1656842.83it/s]
12694248it [00:08, 1674893.53it/s]
12869307it [00:08, 1687887.50it/s]
13042011it [00:08, 1699542.57it/s]
13216789it [00:08, 1713937.96it/s]
13392739it [00:08, 1727550.08it/s]
13569077it [00:08, 1738241.04it/s]
13744353it [00:09, 1742574.94it/s]
13919913it [00:09, 1746459.13it/s]
14094566it [00:09, 1745606.25it/s]
14271090it [00:09, 1751471.90it/s]
14447433it [00:09, 1755038.87it/s]
14625302it [00:09, 1762112.81it/s]
14801516it [00:09, 1755104.95it/s]
14979249it [00:09, 1761731.58it/s]
15157691it [00:09, 1768392.97it/s]
15335973it [00:09, 1772680.77it/s]
15513247it [00:10, 1757262.32it/s]
15687200it [00:10, 1542369.86it/s]
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
tabix -s 1 -b 2 -e 2 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz
seqtool depth_hist -nbins 500 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.depth_hist.tsv
cat 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz> 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.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: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
cat 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md/qc_complete.txt
+ merge_qc -folders 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv
+ head -n1 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv