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

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/6ceae0f235355363d7429056e853c5/.command.log
Size: 8.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:CTATSPLICING_STARTOCANCERINTRONS (rna_s1221_S42)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/a0f89b39dab3e31a4376f94755f168/rna_s1221_S42.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/45/6ceae0f235355363d7429056e853c5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/3c15023005fc6ecaab130723455b3f/rna_s1221_S42.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/3c15023005fc6ecaab130723455b3f/rna_s1221_S42.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/3c15023005fc6ecaab130723455b3f/rna_s1221_S42.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/6ceae0f235355363d7429056e853c5/.command.run
==> STAGING COMPLETE (7 inputs)

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 
Done with chr chr1.
Done with chr chr2.
Done with chr chr4.
Done with chr chr5.
Done with chr chr6.
Done with chr chr7.
Done with chr chr8.
Done with chr chr12.
Done with chr chr16.
Done with chr chr17.
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.