Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/35c0e724ee5ae49cc30c6ed85ccc98/tih_rna_sample_00598_B23MVV7LT4_1.md.bam
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/8d/be8fb507ab60e53e9e4e283d496966/.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/8d/be8fb507ab60e53e9e4e283d496966/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/35c0e724ee5ae49cc30c6ed85ccc98/tih_rna_sample_00598_B23MVV7LT4_1.md.bai
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_00598_B23MVV7LT4_1
+ all_qc -bam tih_rna_sample_00598_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_00598_B23MVV7LT4_1 -reference ref_genome.fa -region chr20
mkdir -p tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/full_bed.bed
seqtool depth -bam tih_rna_sample_00598_B23MVV7LT4_1.md.bam -bed tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth.gz
saturation_plot -bams tih_rna_sample_00598_B23MVV7LT4_1.md.bam -region chr20 -output tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00598_B23MVV7LT4_1.md.bam > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/saturation_qc.tsv
fragment_size -bams tih_rna_sample_00598_B23MVV7LT4_1.md.bam -region chr20 -output_prefix tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bam > tih_rna_sample_00598_B23MVV7LT4_1.md.mpileup && contamination -input tih_rna_sample_00598_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
152513it [00:00, 1524956.94it/s]
320357it [00:00, 1614947.88it/s]
489157it [00:00, 1648170.67it/s]
662117it [00:00, 1680272.07it/s]
839604it [00:00, 1714336.47it/s]
1016344it [00:00, 1732332.30it/s]
1193478it [00:00, 1745046.40it/s]
1369724it [00:00, 1750555.70it/s]
1548787it [00:00, 1763051.81it/s]
1727983it [00:01, 1771946.43it/s]
1905178it [00:01, 1749080.80it/s]
2081790it [00:01, 1754187.65it/s]
2260226it [00:01, 1763240.14it/s]
2436904it [00:01, 1764264.63it/s]
2613360it [00:01, 1753381.31it/s]
2790162it [00:01, 1757724.18it/s]
2969045it [00:01, 1767001.18it/s]
3145768it [00:01, 1749136.04it/s]
3322065it [00:01, 1753217.68it/s]
3497427it [00:02, 1735313.21it/s]
3673809it [00:02, 1743743.48it/s]
3848235it [00:02, 1669097.55it/s]
4015810it [00:02, 1594381.98it/s]
4176219it [00:02, 1519296.16it/s]
4329246it [00:02, 1450755.68it/s]
4486878it [00:02, 1485166.02it/s]
4660926it [00:02, 1557016.17it/s]
4817827it [00:02, 1557486.19it/s]
4974417it [00:02, 1516101.28it/s]
5152832it [00:03, 1593066.03it/s]
5331976it [00:03, 1650755.38it/s]
5511122it [00:03, 1692038.56it/s]
5689210it [00:03, 1718260.45it/s]
5869182it [00:03, 1742390.80it/s]
6051101it [00:03, 1765226.77it/s]
6231753it [00:03, 1777387.18it/s]
6412287it [00:03, 1785707.82it/s]
6592501it [00:03, 1790590.52it/s]
6771660it [00:03, 1761938.59it/s]
6948023it [00:04, 1749191.76it/s]
7126048it [00:04, 1758345.69it/s]
7301983it [00:04, 1758575.99it/s]
7478190it [00:04, 1759583.60it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
7655014it [00:04, 1762134.34it/s]
7831264it [00:04, 1720439.04it/s]
8003540it [00:04, 1713006.78it/s]
8174997it [00:04, 1705266.56it/s]
8348337it [00:04, 1713550.51it/s]
8522111it [00:05, 1720695.31it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
8701339it [00:05, 1741983.21it/s]
8878427it [00:05, 1750578.47it/s]
8981284it [00:05, 1704623.01it/s]
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
tabix -s 1 -b 2 -e 2 tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth.gz
seqtool depth_hist -nbins 500 tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth.gz > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth_hist.tsv
cat tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00598_B23MVV7LT4_1.md -output tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bam > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bam > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth.gz> tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bam > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai
cat tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/qc_complete.txt
+ merge_qc -folders tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md -output tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1_full_basic_stats.tsv
+ head -n1 tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1_full_basic_stats.tsv