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/36/ea23c124aad8dbed59d6b605e1150c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/ad185525d9a45aaf9b25d22aca9b40/659_bIB-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/ad185525d9a45aaf9b25d22aca9b40/659_bIB-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/ad185525d9a45aaf9b25d22aca9b40/659_bIB-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/d18446c911f90809469f2be602f1bc/659_bIB-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/ea23c124aad8dbed59d6b605e1150c/.command.run
==> STAGING COMPLETE (7 inputs)
08:41:15 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[8530000], rate=17060000.00/min 08:41:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bIB-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bIB-T1-TRNA-1_B23MHV2LT4_1.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.
-659_bIB-T1-TRNA-1_B23MHV2LT4_1.introns: identified 8560 cancer introns
08:41:56 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bIB-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bIB-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim
08:41:56 : INFO : Running: touch /tmp/nxf.oP5fTpV3us/659_bIB-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok
08:41:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bIB-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bIB-T1-TRNA-1_B23MHV2LT4_1.cancer.introns
08:41:56 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bIB-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bIB-T1-TRNA-1_B23MHV2LT4_1.cancer.introns
08:41:56 : INFO : Running: touch /tmp/nxf.oP5fTpV3us/659_bIB-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok
08:41:56 : INFO : -found 3614 cancer introns
08:41:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bIB-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bIB-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bIB-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:41:56 : INFO : Creating the BED File.
08:42:03 : INFO : Saving Bed File as 659_bIB-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:42:03 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bIB-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bIB-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bIB-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:42:03 : INFO : Running: touch /tmp/nxf.oP5fTpV3us/659_bIB-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok
08:42:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bIB-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bIB-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bIB-T1-TRNA-1_B23MHV2LT4_1
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai