.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS (BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/c242f728c89feaaf2eb67364dae0cc/.command.log
Size: 11.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS (BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/aec77973b89d81529313915b9c4e31/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/c242f728c89feaaf2eb67364dae0cc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ec3a10410562e6c89a0256d8bfdf6b/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ec3a10410562e6c89a0256d8bfdf6b/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/c242f728c89feaaf2eb67364dae0cc/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ec3a10410562e6c89a0256d8bfdf6b/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)

20:13:00 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

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[980000], rate=19600000.00/min 20:13:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim 
Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18.
-BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns: identified 24 cancer introns
20:13:08 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim 
20:13:08 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/prelim_introns.ok
20:13:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5  > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns 
20:13:09 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5  > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns 
20:13:09 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/introns_filtered.ok
20:13:09 : INFO : -found 12 cancer introns
20:13:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns  --cancer_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed 
20:13:09 : INFO :  Creating the BED File.
20:13:10 : INFO : Saving Bed File as BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed
20:13:10 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns  --cancer_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed 
20:13:10 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/intron_igv_bed.ok
20:13:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed  --bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam  --output_prefix BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2 
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
20:13:28 : INFO : Execution Time = 0.30 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed  --bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam  --output_prefix BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2 
20:13:28 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok
20:13:28 : INFO : Running: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.bam
20:13:28 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.bam
20:13:28 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok
20:13:28 : INFO : Running: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.bam
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
20:13:50 : INFO : Execution Time = 0.36 minutes. CMD: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.bam
20:13:50 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/sort_gene_reads.ok
20:13:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam 
Done with chr chr1.
Done with chr chr2.
Done with chr chr6.
Done with chr chr7.
Done with chr chr8.
Done with chr chr12.
Done with chr chr14.
Done with chr chr15.
20:13:54 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam 
20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
20:13:54 : INFO : Running: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp
20:13:54 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp
20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
20:13:54 : INFO : Running: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 
20:13:54 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 
20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
20:13:54 : INFO : Running: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 
20:13:54 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 
20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
20:13:54 : INFO : Running: create_report BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.ctat-splicing.igv.html  --track-config BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2' 
20:13:56 : INFO : Execution Time = 0.03 minutes. CMD: create_report BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.ctat-splicing.igv.html  --track-config BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2' 
20:13:56 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/igv_create_html.ok
20:13:56 : INFO : done.