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

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/274644ff1c0ffe730309f0057410d1/.command.err
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Task: NFCORE_RNAFUSION:RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS (BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2)
Attempt
Content

07:28:29 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

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[980000], rate=14700000.00/min 07:28:39 : 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
07:28:40 : 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 
07:28:40 : INFO : Running: touch /tmp/nxf.xLpTM1IEjH/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/prelim_introns.ok
07:28:40 : 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 
07:28:40 : 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 
07:28:40 : INFO : Running: touch /tmp/nxf.xLpTM1IEjH/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/introns_filtered.ok
07:28:40 : INFO : -found 12 cancer introns
07:28:40 : 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 
07:28:40 : INFO :  Creating the BED File.
07:28:41 : INFO : Saving Bed File as BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed
07:28:41 : 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 
07:28:41 : INFO : Running: touch /tmp/nxf.xLpTM1IEjH/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/intron_igv_bed.ok
07:28:41 : 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
07:29:03 : INFO : Execution Time = 0.37 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 
07:29:03 : INFO : Running: touch /tmp/nxf.xLpTM1IEjH/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok
07:29:03 : 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
07:29:03 : 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
07:29:03 : INFO : Running: touch /tmp/nxf.xLpTM1IEjH/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok
07:29:03 : 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...
07:29:29 : INFO : Execution Time = 0.43 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
07:29:29 : INFO : Running: touch /tmp/nxf.xLpTM1IEjH/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/sort_gene_reads.ok
07:29:29 : 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 
07:29:33 : 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 
07:29:33 : INFO : Running: touch /tmp/nxf.xLpTM1IEjH/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
07:29:33 : 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
07:29:33 : 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
07:29:33 : INFO : Running: touch /tmp/nxf.xLpTM1IEjH/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:29:33 : INFO : Running: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 
07:29:33 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 
07:29:33 : INFO : Running: touch /tmp/nxf.xLpTM1IEjH/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
07:29:33 : INFO : Running: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 
07:29:33 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 
07:29:33 : INFO : Running: touch /tmp/nxf.xLpTM1IEjH/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
07:29:33 : 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' 
07:29:35 : 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' 
07:29:35 : INFO : Running: touch /tmp/nxf.xLpTM1IEjH/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/igv_create_html.ok
07:29:35 : INFO : done.