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/a0/b6fd7022b780fe193fdd707924365b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/cc6559a3952a0c2158777035fd6e0b/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
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/4c/cc6559a3952a0c2158777035fd6e0b/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bam
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/a0/b6fd7022b780fe193fdd707924365b/.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 FFPE_V4_0002_RNA_0006_A23WJ53LT4_1
+ all_qc -bam FFPE_V4_0002_RNA_0006_A23WJ53LT4_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 FFPE_V4_0002_RNA_0006_A23WJ53LT4_1 -reference ref_genome.fa -region chr20
mkdir -p FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/full_bed.bed
seqtool depth -bam FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bam -bed FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.depth.gz
saturation_plot -bams FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bam -region chr20 -output FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bam > FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/saturation_qc.tsv
fragment_size -bams FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bam -region chr20 -output_prefix FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bam > FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.mpileup && contamination -input FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_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: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
0it [00:00, ?it/s]
150182it [00:00, 1501753.40it/s]
308951it [00:00, 1552034.39it/s]
470984it [00:00, 1583194.64it/s]
637353it [00:00, 1614869.81it/s]
804137it [00:00, 1633949.10it/s]
968845it [00:00, 1638375.35it/s]
1132683it [00:00, 1633990.06it/s]
1296920it [00:00, 1636634.75it/s]
1460681it [00:00, 1636923.88it/s]
1625054it [00:01, 1638846.50it/s]
1790300it [00:01, 1642994.92it/s]
1954601it [00:01, 1642874.93it/s]
2118890it [00:01, 1633816.22it/s]
2289863it [00:01, 1656637.31it/s]
2457168it [00:01, 1661556.47it/s]
2623647it [00:01, 1662513.97it/s]
2789909it [00:01, 1661273.73it/s]
2956044it [00:01, 1657872.16it/s]
3121838it [00:01, 1648463.95it/s]
3286699it [00:02, 1634388.86it/s]
3451289it [00:02, 1637793.72it/s]
3617861it [00:02, 1646030.95it/s]
3786209it [00:02, 1657196.79it/s]
3951951it [00:02, 1649632.86it/s]
4117467it [00:02, 1651268.19it/s]
4282610it [00:02, 1650752.48it/s]
4447706it [00:02, 1650797.36it/s]
4612794it [00:02, 1642260.91it/s]
4777034it [00:02, 1640912.16it/s]
4941989it [00:03, 1643394.87it/s]
5106336it [00:03, 1627223.90it/s]
5272621it [00:03, 1637788.33it/s]
5441011it [00:03, 1651504.40it/s]
5610241it [00:03, 1663659.57it/s]
5779059it [00:03, 1670840.69it/s]
5946225it [00:03, 1671063.74it/s]
6115597it [00:03, 1677825.14it/s]
6284883it [00:03, 1682306.98it/s]
6453123it [00:03, 1676501.44it/s]
6620784it [00:04, 1672161.67it/s]
6788009it [00:04, 1663954.12it/s]
6954888it [00:04, 1665379.80it/s]
7121767it [00:04, 1666383.46it/s]
7288413it [00:04, 1663977.99it/s]
7454816it [00:04, 1663928.77it/s]
7622059it [00:04, 1666387.08it/s]
7788701it [00:04, 1660861.02it/s]
7954793it [00:04, 1654852.76it/s]
8120690it [00:04, 1656066.96it/s]
8287474it [00:05, 1659569.30it/s]
8457203it [00:05, 1670841.61it/s]
8625642it [00:05, 1674885.26it/s]
8793136it [00:05, 1662653.72it/s]
8959425it [00:05, 1641298.59it/s]
9123622it [00:05, 1639968.77it/s]
9291906it [00:05, 1652688.70it/s]
9459806it [00:05, 1660513.27it/s]
9626912it [00:05, 1663648.03it/s]
9796436it [00:05, 1673074.36it/s]
9965910it [00:06, 1679543.21it/s]
10137053it [00:06, 1689031.93it/s]
10305970it [00:06, 1681022.97it/s]
10474090it [00:06, 1662589.91it/s]
10640400it [00:06, 1656356.16it/s]
10806071it [00:06, 1650518.45it/s]
10974482it [00:06, 1660482.82it/s]
11140557it [00:06, 1657971.64it/s]
11306372it [00:06, 1656037.56it/s]
11471988it [00:06, 1648090.03it/s]
11636811it [00:07, 1639331.82it/s]
11802834it [00:07, 1645435.11it/s]
11967393it [00:07, 1638391.61it/s]
12135178it [00:07, 1649956.42it/s]
12302104it [00:07, 1655703.95it/s]
12467690it [00:07, 1654513.00it/s]
12635919it [00:07, 1662805.65it/s]
12806162it [00:07, 1674652.33it/s]
12973637it [00:07, 1670081.71it/s]
13140654it [00:07, 1666864.69it/s]
13307348it [00:08, 1666724.92it/s]
13474026it [00:08, 1660871.40it/s]
13640120it [00:08, 1658923.88it/s]
13722355it [00:08, 1653471.10it/s]
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
tabix -s 1 -b 2 -e 2 FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.depth.gz
seqtool depth_hist -nbins 500 FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.depth.gz > FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.depth_hist.tsv
cat FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md -output FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/FFPE_V4_0002_RNA_0006_A23WJ53LT4_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 FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bam > FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_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 FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bam > FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.depth.gz> FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_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 FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bam > FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_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: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md.bai
cat FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md/qc_complete.txt
+ merge_qc -folders FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.md -output FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1_full_basic_stats.tsv
+ head -n1 FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed FFPE_V4_0002_RNA_0006_A23WJ53LT4_1/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1_full_basic_stats.tsv