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/12/201ba3fee02139ae52230b9e7ed303/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/024336e116bc083ef08a44cd1b0a70/tih_rna_sample_00586_B23MVV7LT4_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-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/024336e116bc083ef08a44cd1b0a70/tih_rna_sample_00586_B23MVV7LT4_1.md.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/201ba3fee02139ae52230b9e7ed303/.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 tih_rna_sample_00586_B23MVV7LT4_1
+ all_qc -bam tih_rna_sample_00586_B23MVV7LT4_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 tih_rna_sample_00586_B23MVV7LT4_1 -reference ref_genome.fa -region chr20
mkdir -p tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/full_bed.bed
seqtool depth -bam tih_rna_sample_00586_B23MVV7LT4_1.md.bam -bed tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/tih_rna_sample_00586_B23MVV7LT4_1.md.depth.gz
saturation_plot -bams tih_rna_sample_00586_B23MVV7LT4_1.md.bam -region chr20 -output tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00586_B23MVV7LT4_1.md.bam > tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/saturation_qc.tsv
fragment_size -bams tih_rna_sample_00586_B23MVV7LT4_1.md.bam -region chr20 -output_prefix tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed tih_rna_sample_00586_B23MVV7LT4_1.md.bam > tih_rna_sample_00586_B23MVV7LT4_1.md.mpileup && contamination -input tih_rna_sample_00586_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_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: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
0it [00:00, ?it/s]
132268it [00:00, 1322589.82it/s]
265229it [00:00, 1326677.17it/s]
409570it [00:00, 1379802.96it/s]
553270it [00:00, 1402355.66it/s]
702076it [00:00, 1433228.69it/s]
863510it [00:00, 1494776.65it/s]
1028636it [00:00, 1545891.51it/s]
1191724it [00:00, 1572918.15it/s]
1351947it [00:00, 1582046.12it/s]
1514795it [00:01, 1596356.30it/s]
1674431it [00:01, 1535559.27it/s]
1832649it [00:01, 1549334.22it/s]
1996972it [00:01, 1577215.28it/s]
2162207it [00:01, 1599586.38it/s]
2329770it [00:01, 1622269.92it/s]
2492193it [00:01, 1618756.03it/s]
2654205it [00:01, 1609459.72it/s]
2815254it [00:01, 1582868.12it/s]
2973691it [00:01, 1549600.64it/s]
3128860it [00:02, 1531525.61it/s]
3282161it [00:02, 1518738.77it/s]
3443577it [00:02, 1546589.54it/s]
3598375it [00:02, 1443670.82it/s]
3744095it [00:02, 1377546.02it/s]
3883145it [00:02, 1333053.06it/s]
4017391it [00:02, 1287279.29it/s]
4146818it [00:02, 1262051.77it/s]
4301910it [00:02, 1342416.46it/s]
4456975it [00:03, 1401499.37it/s]
4615186it [00:03, 1453592.44it/s]
4781339it [00:03, 1514294.60it/s]
4939248it [00:03, 1533345.35it/s]
5100919it [00:03, 1557996.54it/s]
5260115it [00:03, 1568053.74it/s]
5417235it [00:03, 1531144.73it/s]
5574156it [00:03, 1542290.22it/s]
5732619it [00:03, 1554774.94it/s]
5888327it [00:03, 1545727.99it/s]
6046155it [00:04, 1555344.15it/s]
6201817it [00:04, 1401769.52it/s]
6359998it [00:04, 1451598.45it/s]
6507599it [00:04, 1378970.26it/s]
6656690it [00:04, 1409939.65it/s]
6807923it [00:04, 1438935.85it/s]
6957430it [00:04, 1454743.50it/s]
7105314it [00:04, 1461745.55it/s]
7261649it [00:04, 1491599.93it/s]
7427533it [00:04, 1541047.43it/s]
7593562it [00:05, 1576445.46it/s]
7754459it [00:05, 1586027.66it/s]
7913333it [00:05, 1575318.23it/s]
8076068it [00:05, 1590738.89it/s]
8239050it [00:05, 1602370.54it/s]
8405811it [00:05, 1621659.32it/s]
8568066it [00:05, 1569284.98it/s]
8605923it [00:05, 1505093.59it/s]
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
tabix -s 1 -b 2 -e 2 tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/tih_rna_sample_00586_B23MVV7LT4_1.md.depth.gz
seqtool depth_hist -nbins 500 tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/tih_rna_sample_00586_B23MVV7LT4_1.md.depth.gz > tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/tih_rna_sample_00586_B23MVV7LT4_1.md.depth_hist.tsv
cat tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/tih_rna_sample_00586_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00586_B23MVV7LT4_1.md -output tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/tih_rna_sample_00586_B23MVV7LT4_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 tih_rna_sample_00586_B23MVV7LT4_1.md.bam > tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_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 tih_rna_sample_00586_B23MVV7LT4_1.md.bam > tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/tih_rna_sample_00586_B23MVV7LT4_1.md.depth.gz> tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_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 tih_rna_sample_00586_B23MVV7LT4_1.md.bam > tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_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: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.md.bai
cat tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "tih_rna_sample_00586_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md/qc_complete.txt
+ merge_qc -folders tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1.md -output tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1_full_basic_stats.tsv
+ head -n1 tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00586_B23MVV7LT4_1/tih_rna_sample_00586_B23MVV7LT4_1_full_basic_stats.tsv