Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/eec3bf2e240c86ba840a23a53bd86e/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.Chimeric.out.junction
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/3b/7fdb301642c8f15b45a871fffeca5c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/eec3bf2e240c86ba840a23a53bd86e/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/8c487a2ff541fb2e5b7a3abc6909ee/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/7fdb301642c8f15b45a871fffeca5c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/eec3bf2e240c86ba840a23a53bd86e/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.SJ.out.tab
==> STAGING COMPLETE (7 inputs)
08:28:56 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[12620000], rate=20464864.86/min 08:29:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_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.
-1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns: identified 5452 cancer introns
08:29:43 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim
08:29:43 : INFO : Running: touch /tmp/nxf.6VHWeKazhv/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/prelim_introns.ok
08:29:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns
08:29:43 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns
08:29:43 : INFO : Running: touch /tmp/nxf.6VHWeKazhv/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/introns_filtered.ok
08:29:43 : INFO : -found 1748 cancer introns
08:29:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
08:29:43 : INFO : Creating the BED File.
08:29:47 : INFO : Saving Bed File as 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
08:29:47 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
08:29:47 : INFO : Running: touch /tmp/nxf.6VHWeKazhv/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/intron_igv_bed.ok
08:29:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2
[W::hts_idx_load3] The index file is older than the data file: 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
08:44:14 : INFO : Execution Time = 14.45 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2
08:44:14 : INFO : Running: touch /tmp/nxf.6VHWeKazhv/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/reads_alignments_extracted.ok
08:44:15 : INFO : Running: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam
08:44:15 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam
08:44:15 : INFO : Running: touch /tmp/nxf.6VHWeKazhv/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_cancer_intron_reads.ok
08:44:15 : INFO : Running: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam
[bam_sort_core] merging from 78 files and 1 in-memory blocks...