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/bf/3ddee561adb6146757aa4bdec45126/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/ed167b63bb67bdf6ac399ab10595bc/FFPE_HD789_01_RNA_13_A23YTGFLT4_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/0c/ed167b63bb67bdf6ac399ab10595bc/FFPE_HD789_01_RNA_13_A23YTGFLT4_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/bf/3ddee561adb6146757aa4bdec45126/.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_HD789_01_RNA_13_A23YTGFLT4_1
+ all_qc -bam FFPE_HD789_01_RNA_13_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 FFPE_HD789_01_RNA_13_A23YTGFLT4_1 -reference ref_genome.fa -region chr20
mkdir -p FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/full_bed.bed
seqtool depth -bam FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bam -bed FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.depth.gz
saturation_plot -bams FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bam -region chr20 -output FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bam > FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/saturation_qc.tsv
fragment_size -bams FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bam -region chr20 -output_prefix FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_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 FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bam > FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.mpileup && contamination -input FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_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: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
0it [00:00, ?it/s]
146346it [00:00, 1463346.26it/s]
309558it [00:00, 1562591.95it/s]
477796it [00:00, 1617265.99it/s]
644100it [00:00, 1635318.75it/s]
814077it [00:00, 1658537.56it/s]
984516it [00:00, 1674109.95it/s]
1153693it [00:00, 1679869.42it/s]
1324621it [00:00, 1689216.00it/s]
1493543it [00:00, 1687651.75it/s]
1666233it [00:01, 1699746.04it/s]
1836209it [00:01, 1699216.66it/s]
2008667it [00:01, 1706912.71it/s]
2179360it [00:01, 1700104.93it/s]
2352078it [00:01, 1708240.02it/s]
2525138it [00:01, 1714950.07it/s]
2696890it [00:01, 1715613.53it/s]
2868456it [00:01, 1711902.30it/s]
3043500it [00:01, 1723441.69it/s]
3215851it [00:01, 1714829.40it/s]
3387347it [00:02, 1698494.98it/s]
3557234it [00:02, 1694579.81it/s]
3729276it [00:02, 1702255.18it/s]
3899569it [00:02, 1702443.62it/s]
4070312it [00:02, 1703886.61it/s]
4240723it [00:02, 1703939.34it/s]
4413535it [00:02, 1711164.75it/s]
4588031it [00:02, 1721225.52it/s]
4760161it [00:02, 1718995.69it/s]
4932391it [00:02, 1719974.81it/s]
5104393it [00:03, 1715972.61it/s]
5275995it [00:03, 1688574.02it/s]
5444948it [00:03, 1687885.19it/s]
5615371it [00:03, 1692713.80it/s]
5787341it [00:03, 1700710.21it/s]
5958603it [00:03, 1704152.80it/s]
6129183it [00:03, 1704619.06it/s]
6299667it [00:03, 1695978.24it/s]
6469288it [00:03, 1690977.76it/s]
6642543it [00:03, 1703357.58it/s]
6812898it [00:04, 1700141.90it/s]
6983269it [00:04, 1701196.22it/s]
7155970it [00:04, 1708905.95it/s]
7326870it [00:04, 1704836.13it/s]
7498098it [00:04, 1707051.86it/s]
7670795it [00:04, 1712875.34it/s]
7842089it [00:04, 1712474.51it/s]
8013885it [00:04, 1713987.53it/s]
8185287it [00:04, 1713934.06it/s]
8358170it [00:04, 1718373.21it/s]
8530009it [00:05, 1717192.86it/s]
8702655it [00:05, 1719822.46it/s]
8874639it [00:05, 1717709.01it/s]
9046412it [00:05, 1711601.43it/s]
9219631it [00:05, 1717746.40it/s]
9392202it [00:05, 1720117.97it/s]
9564272it [00:05, 1720281.72it/s]
9736304it [00:05, 1713780.19it/s]
9907690it [00:05, 1711559.84it/s]
10079860it [00:05, 1714579.95it/s]
10251323it [00:06, 1706701.29it/s]
10422003it [00:06, 1704214.26it/s]
10592431it [00:06, 1702480.19it/s]
10763899it [00:06, 1706058.50it/s]
10937241it [00:06, 1714234.14it/s]
11108670it [00:06, 1710548.84it/s]
11281209it [00:06, 1714897.27it/s]
11452985it [00:06, 1715741.36it/s]
11624563it [00:06, 1712097.14it/s]
11795777it [00:06, 1699674.50it/s]
11965765it [00:07, 1693541.78it/s]
12136761it [00:07, 1698418.30it/s]
12306682it [00:07, 1698640.57it/s]
12477014it [00:07, 1700026.47it/s]
12647025it [00:07, 1699368.16it/s]
12817832it [00:07, 1701961.67it/s]
12988033it [00:07, 1701660.64it/s]
13158202it [00:07, 1697299.66it/s]
13329042it [00:07, 1700610.67it/s]
13499237it [00:07, 1701001.29it/s]
13669340it [00:08, 1700327.77it/s]
13841586it [00:08, 1706950.34it/s]
14012284it [00:08, 1687177.97it/s]
14183541it [00:08, 1694716.43it/s]
14353812it [00:08, 1697088.23it/s]
14523553it [00:08, 1694658.78it/s]
14694341it [00:08, 1698544.21it/s]
14864213it [00:08, 1695821.55it/s]
15034605it [00:08, 1698231.81it/s]
15057187it [00:08, 1701365.30it/s]
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
tabix -s 1 -b 2 -e 2 FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.depth.gz
seqtool depth_hist -nbins 500 FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.depth.gz > FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.depth_hist.tsv
cat FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md -output FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/FFPE_HD789_01_RNA_13_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 FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bam > FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_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 FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bam > FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_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 FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.depth.gz> FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_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 FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bam > FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_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: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md.bai
cat FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md/qc_complete.txt
+ merge_qc -folders FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.md -output FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1_full_basic_stats.tsv
+ head -n1 FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed FFPE_HD789_01_RNA_13_A23YTGFLT4_1/FFPE_HD789_01_RNA_13_A23YTGFLT4_1_full_basic_stats.tsv