Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/4d60d2b69965052c8400e0026ff4df/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_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/7f/9b566de3a18f54daa1a2a49889d003/.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/7f/9b566de3a18f54daa1a2a49889d003/.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-rnd-pltf-dev-nextflow-scratch-01/work/68/4d60d2b69965052c8400e0026ff4df/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
  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_CRX_T1_RNA_SLD_01_A23T55JLT4_1
+ all_qc -bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_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 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1 -reference ref_genome.fa -region chr20
mkdir -p 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/


cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed


seqtool depth -bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz
seqtool saturation_metric       -at 1000000       -region chr20       -bam_threads 1       1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_qc.tsv 
fragment_size       -bams 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam       -region chr20       -output_prefix 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/fragsize       -threads 1 
samtools mpileup   -B --min-MQ 60 --min-BQ 30    -f ref_genome.fa   -l dbsnp_hg38_contam_sites.bed   1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup && contamination -input 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/contamination.tsv 
saturation_plot       -bams 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam       -region chr20       -output 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_plot.png       -threads 1 
[mpileup] 1 samples in 1 input files
/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



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tabix -s 1 -b 2 -e 2 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz


seqtool depth_hist     -nbins 500     1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz     > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv


cat 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv | plot         -x 0         -xlabel Depth -ylabel "Number of Sites"         -xlim 0 2000         -title 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md         -output 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.png




seqtool reads_per_target     -bed Twist_rna_exome_AND_fusion_hg38.bed     -threads 1     -bam_threads 2     1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv 
seqtool read_qc    -bed Twist_rna_exome_AND_fusion_hg38.bed     -n_threads 1     -bam_threads 2     1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/read_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats  -bed Twist_rna_exome_AND_fusion_hg38.bed  1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz> 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_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  1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam  > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv 




cat 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 






echo `date` > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md/qc_complete.txt


+ merge_qc -folders 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv
+ head -n1 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv