.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS (rna_s1221_S42)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/6ceae0f235355363d7429056e853c5/.command.err
Size: 7.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS (rna_s1221_S42)
Attempt
Content

13:04:16 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

[190000], rate=11400000.00/min 
[200000], rate=12000000.00/min 
[210000], rate=12600000.00/min 
[220000], rate=13200000.00/min 
[230000], rate=13800000.00/min 
[240000], rate=14400000.00/min 
[250000], rate=15000000.00/min 
[260000], rate=15600000.00/min 
[270000], rate=16200000.00/min 
[280000], rate=16800000.00/min 
[290000], rate=17400000.00/min 
[300000], rate=18000000.00/min 
[310000], rate=18600000.00/min 
[320000], rate=19200000.00/min 
[330000], rate=19800000.00/min 
[340000], rate=20400000.00/min 
[350000], rate=21000000.00/min 
[360000], rate=21600000.00/min 
[370000], rate=22200000.00/min 
[380000], rate=22800000.00/min 
[390000], rate=23400000.00/min 
[400000], rate=24000000.00/min 
[410000], rate=24600000.00/min 
[420000], rate=25200000.00/min 
[430000], rate=25800000.00/min 
[440000], rate=26400000.00/min 
[450000], rate=27000000.00/min 
[460000], rate=27600000.00/min 
[470000], rate=28200000.00/min 
[480000], rate=28800000.00/min 
[490000], rate=29400000.00/min 
[500000], rate=30000000.00/min 
[510000], rate=30600000.00/min 
[520000], rate=31200000.00/min 
[530000], rate=31800000.00/min 
[540000], rate=32400000.00/min 13:04:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1221_S42.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > rna_s1221_S42.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.
-rna_s1221_S42.introns: identified 1037 cancer introns
13:04:21 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1221_S42.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > rna_s1221_S42.cancer.introns.prelim 
13:04:21 : INFO : Running: touch /tmp/nxf.W4njRjh1Ov/rna_s1221_S42.chckpts/prelim_introns.ok
13:04:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1221_S42.cancer.introns.prelim --min_total_reads 5  > rna_s1221_S42.cancer.introns 
13:04:21 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1221_S42.cancer.introns.prelim --min_total_reads 5  > rna_s1221_S42.cancer.introns 
13:04:21 : INFO : Running: touch /tmp/nxf.W4njRjh1Ov/rna_s1221_S42.chckpts/introns_filtered.ok
13:04:21 : INFO : -found 19 cancer introns
13:04:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1221_S42.introns  --cancer_introns rna_s1221_S42.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed rna_s1221_S42.introns.for_IGV.bed 
13:04:21 : INFO :  Creating the BED File.
13:04:22 : INFO : Saving Bed File as rna_s1221_S42.introns.for_IGV.bed
13:04:22 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1221_S42.introns  --cancer_introns rna_s1221_S42.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed rna_s1221_S42.introns.for_IGV.bed 
13:04:22 : INFO : Running: touch /tmp/nxf.W4njRjh1Ov/rna_s1221_S42.chckpts/intron_igv_bed.ok
13:04:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1221_S42.introns.for_IGV.bed  --bam rna_s1221_S42.Aligned.sortedByCoord.out.bam  --output_prefix rna_s1221_S42 
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
13:04:22 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1221_S42.introns.for_IGV.bed  --bam rna_s1221_S42.Aligned.sortedByCoord.out.bam  --output_prefix rna_s1221_S42 
13:04:22 : INFO : Running: touch /tmp/nxf.W4njRjh1Ov/rna_s1221_S42.chckpts/reads_alignments_extracted.ok
13:04:22 : INFO : Running: samtools sort -o rna_s1221_S42.cancer_intron_reads.sorted.bam rna_s1221_S42.cancer_intron_reads.bam
13:04:22 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1221_S42.cancer_intron_reads.sorted.bam rna_s1221_S42.cancer_intron_reads.bam
13:04:22 : INFO : Running: touch /tmp/nxf.W4njRjh1Ov/rna_s1221_S42.chckpts/sort_cancer_intron_reads.ok
13:04:22 : INFO : Running: samtools sort -o rna_s1221_S42.gene_reads.sorted.bam rna_s1221_S42.gene_reads.bam
13:04:23 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o rna_s1221_S42.gene_reads.sorted.bam rna_s1221_S42.gene_reads.bam
13:04:23 : INFO : Running: touch /tmp/nxf.W4njRjh1Ov/rna_s1221_S42.chckpts/sort_gene_reads.ok
13:04:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  rna_s1221_S42.gene_reads.sorted.bam 
13:04:23 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  rna_s1221_S42.gene_reads.sorted.bam 
13:04:23 : INFO : Running: touch /tmp/nxf.W4njRjh1Ov/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp.ok
13:04:23 : INFO : Running: samtools sort -o rna_s1221_S42.gene_reads.sorted.sifted.bam rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp
13:04:23 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1221_S42.gene_reads.sorted.sifted.bam rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp
13:04:23 : INFO : Running: touch /tmp/nxf.W4njRjh1Ov/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.tmpsorted.ok
13:04:23 : INFO : Running: samtools index rna_s1221_S42.gene_reads.sorted.sifted.bam 
13:04:23 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1221_S42.gene_reads.sorted.sifted.bam 
13:04:23 : INFO : Running: touch /tmp/nxf.W4njRjh1Ov/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.indexed.ok
13:04:23 : INFO : Running: samtools index rna_s1221_S42.cancer_intron_reads.sorted.bam 
13:04:23 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1221_S42.cancer_intron_reads.sorted.bam 
13:04:23 : INFO : Running: touch /tmp/nxf.W4njRjh1Ov/rna_s1221_S42.chckpts/rna_s1221_S42.cancer_intron_reads.sorted.bam.indexed.ok
13:04:23 : INFO : Running: create_report rna_s1221_S42.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output rna_s1221_S42.ctat-splicing.igv.html  --track-config rna_s1221_S42.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: rna_s1221_S42' 
13:04:25 : INFO : Execution Time = 0.03 minutes. CMD: create_report rna_s1221_S42.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output rna_s1221_S42.ctat-splicing.igv.html  --track-config rna_s1221_S42.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: rna_s1221_S42' 
13:04:25 : INFO : Running: touch /tmp/nxf.W4njRjh1Ov/rna_s1221_S42.chckpts/igv_create_html.ok
13:04:25 : INFO : done.