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/55/9e8f715a9eda2d5ac9fc50d174e413/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/bc077b0451b14e0f9358989e078f2c/tih_rna_sample_00479_B23WHTKLT4_2.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/9e8f715a9eda2d5ac9fc50d174e413/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/bc077b0451b14e0f9358989e078f2c/tih_rna_sample_00479_B23WHTKLT4_2.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/7ae8a5a4afba700f931a84749e4ede/tih_rna_sample_00479_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/bc077b0451b14e0f9358989e078f2c/tih_rna_sample_00479_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (7 inputs)
08:24:37 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[5430000], rate=18100000.00/min
[5440000], rate=18133333.33/min
[5450000], rate=18166666.67/min
[5460000], rate=18200000.00/min
[5470000], rate=18233333.33/min
[5480000], rate=18266666.67/min
[5490000], rate=18300000.00/min
[5500000], rate=18333333.33/min
[5510000], rate=18366666.67/min
[5520000], rate=18400000.00/min
[5530000], rate=18433333.33/min
[5540000], rate=18466666.67/min
[5550000], rate=18500000.00/min
[5560000], rate=18533333.33/min
[5570000], rate=18566666.67/min
[5580000], rate=18600000.00/min
[5590000], rate=18633333.33/min
[5600000], rate=18666666.67/min
[5610000], rate=17715789.47/min
[5620000], rate=17747368.42/min
[5630000], rate=17778947.37/min
[5640000], rate=17810526.32/min
[5650000], rate=17842105.26/min
[5660000], rate=17873684.21/min
[5670000], rate=17905263.16/min
[5680000], rate=17936842.11/min
[5690000], rate=17968421.05/min
[5700000], rate=18000000.00/min
[5710000], rate=18031578.95/min
[5720000], rate=18063157.89/min
[5730000], rate=18094736.84/min
[5740000], rate=18126315.79/min
[5750000], rate=18157894.74/min
[5760000], rate=18189473.68/min
[5770000], rate=18221052.63/min
[5780000], rate=18252631.58/min
[5790000], rate=18284210.53/min
[5800000], rate=18315789.47/min
[5810000], rate=18347368.42/min
[5820000], rate=18378947.37/min
[5830000], rate=18410526.32/min
[5840000], rate=18442105.26/min
[5850000], rate=18473684.21/min
[5860000], rate=18505263.16/min 08:25:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00479_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00479_B23WHTKLT4_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.
-tih_rna_sample_00479_B23WHTKLT4_2.introns: identified 7131 cancer introns
08:25:06 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00479_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns.prelim
08:25:06 : INFO : Running: touch /tmp/nxf.xoIag8UAcV/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/prelim_introns.ok
08:25:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns
08:25:06 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns
08:25:06 : INFO : Running: touch /tmp/nxf.xoIag8UAcV/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/introns_filtered.ok
08:25:06 : INFO : -found 2663 cancer introns
08:25:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00479_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed
08:25:06 : INFO : Creating the BED File.
08:25:11 : INFO : Saving Bed File as tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed
08:25:11 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00479_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed
08:25:11 : INFO : Running: touch /tmp/nxf.xoIag8UAcV/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/intron_igv_bed.ok
08:25:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00479_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00479_B23WHTKLT4_2
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00479_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam.bai
08:38:19 : INFO : Execution Time = 13.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00479_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00479_B23WHTKLT4_2
08:38:19 : INFO : Running: touch /tmp/nxf.xoIag8UAcV/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/reads_alignments_extracted.ok
08:38:19 : INFO : Running: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00479_B23WHTKLT4_2.cancer_intron_reads.bam
08:38:19 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00479_B23WHTKLT4_2.cancer_intron_reads.bam
08:38:19 : INFO : Running: touch /tmp/nxf.xoIag8UAcV/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/sort_cancer_intron_reads.ok
08:38:19 : INFO : Running: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.bam tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.bam
[bam_sort_core] merging from 75 files and 1 in-memory blocks...