Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/199fb4c062c092ae6b510da73c33e6/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.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/63/589dc9ba2eae00d6eb6d9a74e04761/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/199fb4c062c092ae6b510da73c33e6/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.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/63/589dc9ba2eae00d6eb6d9a74e04761/.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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2
+ all_qc -bam 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2 -reference ref_genome.fa -region chr20
mkdir -p 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/full_bed.bed
seqtool depth -bam 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -bed 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz
saturation_plot -bams 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -region chr20 -output 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/saturation_qc.tsv
fragment_size -bams 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -region chr20 -output_prefix 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.mpileup && contamination -input 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.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: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
0it [00:00, ?it/s]
144154it [00:00, 1441338.63it/s]
295372it [00:00, 1482937.75it/s]
456930it [00:00, 1543322.45it/s]
620981it [00:00, 1581622.09it/s]
788465it [00:00, 1615174.86it/s]
955735it [00:00, 1634679.31it/s]
1124956it [00:00, 1653249.38it/s]
1298053it [00:00, 1677937.75it/s]
1465847it [00:00, 1665577.30it/s]
1632425it [00:01, 1663245.70it/s]
1798763it [00:01, 1659682.74it/s]
1964741it [00:01, 1619024.31it/s]
2130663it [00:01, 1630878.31it/s]
2297936it [00:01, 1643162.92it/s]
2462388it [00:01, 1628000.27it/s]
2625300it [00:01, 1540409.33it/s]
2791170it [00:01, 1574223.91it/s]
2959269it [00:01, 1605166.84it/s]
3120484it [00:01, 1606840.28it/s]
3282715it [00:02, 1611350.39it/s]
3450874it [00:02, 1632017.74it/s]
3620530it [00:02, 1651173.96it/s]
3787884it [00:02, 1657795.05it/s]
3956168it [00:02, 1665228.81it/s]
4124008it [00:02, 1669124.12it/s]
4291043it [00:02, 1669152.05it/s]
4461305it [00:02, 1679064.58it/s]
4630026it [00:02, 1681463.86it/s]
4798200it [00:02, 1675788.85it/s]
4968169it [00:03, 1682899.99it/s]
5136478it [00:03, 1680896.18it/s]
5305004it [00:03, 1682001.12it/s]
5473214it [00:03, 1678835.37it/s]
5641105it [00:03, 1665254.76it/s]
5808180it [00:03, 1666843.00it/s]
5975297it [00:03, 1668099.16it/s]
6142122it [00:03, 1510020.67it/s]
6302997it [00:03, 1537501.64it/s]
6464666it [00:03, 1559963.45it/s]
6552581it [00:04, 1626635.24it/s]
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
tabix -s 1 -b 2 -e 2 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz
seqtool depth_hist -nbins 500 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.depth_hist.tsv
cat 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz> 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.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: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bai
cat 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md/qc_complete.txt
+ merge_qc -folders 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv
+ head -n1 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv