Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/a079c3293495e6b0304c312fc5c9ff/A673_FFPE_RNA_0001_B23LG7FLT4_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/26/2b7976bdfa672b0ef2d2f758136b7c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/a079c3293495e6b0304c312fc5c9ff/A673_FFPE_RNA_0001_B23LG7FLT4_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/26/2b7976bdfa672b0ef2d2f758136b7c/.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 A673_FFPE_RNA_0001_B23LG7FLT4_1
+ all_qc -bam A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_1 -reference ref_genome.fa -region chr20
mkdir -p A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/full_bed.bed
seqtool depth -bam A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -bed A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz
saturation_plot -bams A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/saturation_qc.tsv
fragment_size -bams A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output_prefix A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1.md.mpileup && contamination -input A673_FFPE_RNA_0001_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_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: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
157903it [00:00, 1578952.45it/s]
323728it [00:00, 1625570.68it/s]
491333it [00:00, 1648602.91it/s]
662282it [00:00, 1672442.30it/s]
833810it [00:00, 1687854.29it/s]
1004571it [00:00, 1694557.58it/s]
1174952it [00:00, 1697569.55it/s]
1344709it [00:00, 1695989.50it/s]
1514309it [00:00, 1690743.17it/s]
1685474it [00:01, 1697167.53it/s]
1856301it [00:01, 1700541.21it/s]
2026359it [00:01, 1697786.37it/s]
2196636it [00:01, 1699281.28it/s]
2367922it [00:01, 1703363.92it/s]
2538261it [00:01, 1699329.06it/s]
2708903it [00:01, 1701282.28it/s]
2879035it [00:01, 1695781.67it/s]
3048748it [00:01, 1696062.40it/s]
3219591it [00:01, 1699756.04it/s]
3389571it [00:02, 1683805.47it/s]
3558146it [00:02, 1684251.13it/s]
3726943it [00:02, 1685278.79it/s]
3897102it [00:02, 1690136.76it/s]
4070648it [00:02, 1703687.28it/s]
4241031it [00:02, 1702122.71it/s]
4411253it [00:02, 1697691.12it/s]
4581710it [00:02, 1699731.75it/s]
4752640it [00:02, 1702443.21it/s]
4922890it [00:02, 1691649.17it/s]
5092073it [00:03, 1683692.06it/s]
5264295it [00:03, 1695091.51it/s]
5435294it [00:03, 1699520.58it/s]
5606418it [00:03, 1703006.08it/s]
5778724it [00:03, 1708921.02it/s]
5949627it [00:03, 1708767.48it/s]
6122606it [00:03, 1715049.14it/s]
6294117it [00:03, 1702698.73it/s]
6464411it [00:03, 1700002.61it/s]
6634428it [00:03, 1689539.50it/s]
6803820it [00:04, 1690776.52it/s]
6972914it [00:04, 1683188.99it/s]
7141647it [00:04, 1684306.95it/s]
7310089it [00:04, 1683144.53it/s]
7478411it [00:04, 1680324.59it/s]
7647983it [00:04, 1684909.65it/s]
7816902it [00:04, 1686175.00it/s]
7986778it [00:04, 1689859.10it/s]
8158235it [00:04, 1697252.66it/s]
8327964it [00:04, 1695242.63it/s]
8499410it [00:05, 1700981.29it/s]
8669511it [00:05, 1697348.55it/s]
8840431it [00:05, 1700883.11it/s]
9010523it [00:05, 1700525.47it/s]
9180578it [00:05, 1697701.51it/s]
9350351it [00:05, 1696978.91it/s]
9520051it [00:05, 1690500.28it/s]
9691303it [00:05, 1697041.07it/s]
9861014it [00:05, 1696207.99it/s]
10030649it [00:05, 1696236.45it/s]
10200276it [00:06, 1693916.00it/s]
10369754it [00:06, 1694157.00it/s]
10539172it [00:06, 1680314.09it/s]
10709151it [00:06, 1686104.68it/s]
10881527it [00:06, 1697334.85it/s]
11051281it [00:06, 1696912.80it/s]
11223014it [00:06, 1703008.34it/s]
11394350it [00:06, 1706096.62it/s]
11568115it [00:06, 1715535.34it/s]
11739676it [00:06, 1713260.13it/s]
11911661it [00:07, 1715134.06it/s]
12083179it [00:07, 1711245.80it/s]
12254309it [00:07, 1709850.89it/s]
12425298it [00:07, 1703426.23it/s]
12597124it [00:07, 1707844.73it/s]
12767915it [00:07, 1702809.43it/s]
12938203it [00:07, 1700759.43it/s]
13108284it [00:07, 1698959.09it/s]
13278337it [00:07, 1699417.14it/s]
13448281it [00:07, 1697816.81it/s]
13619216it [00:08, 1701257.08it/s]
13789344it [00:08, 1694540.17it/s]
13958805it [00:08, 1681588.90it/s]
14126987it [00:08, 1676235.29it/s]
14294626it [00:08, 1674955.43it/s]
14462132it [00:08, 1674887.07it/s]
14550647it [00:08, 1694072.71it/s]
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
tabix -s 1 -b 2 -e 2 A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz
seqtool depth_hist -nbins 500 A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv
cat A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title A673_FFPE_RNA_0001_B23LG7FLT4_1.md -output A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz> A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_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: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
cat A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "A673_FFPE_RNA_0001_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/qc_complete.txt
+ merge_qc -folders A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md -output A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv
+ head -n1 A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv