Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/c3ca5c8022779ac9e9522eacf50a0f/659_cTi-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/c3ca5c8022779ac9e9522eacf50a0f/659_cTi-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
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/25/cfe6745981c23a1f520d998a16adb9/.command.sh
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/c3ca5c8022779ac9e9522eacf50a0f/659_cTi-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/ae87de345fdc8a0c4f903121810bb0/659_cTi-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)
08:45:26 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10620000], rate=8496000.00/min
[10630000], rate=8504000.00/min
[10640000], rate=8512000.00/min
[10650000], rate=8520000.00/min
[10660000], rate=8528000.00/min
[10670000], rate=8536000.00/min
[10680000], rate=8544000.00/min 08:46:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_cTi-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_cTi-T1-TRNA-1_B23MHV2LT4_1.introns: identified 8321 cancer introns
08:46:57 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim
08:46:57 : INFO : Running: touch /tmp/nxf.mXOV0Mklku/659_cTi-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok
08:46:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns
08:46:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns
08:46:57 : INFO : Running: touch /tmp/nxf.mXOV0Mklku/659_cTi-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok
08:46:57 : INFO : -found 2706 cancer introns
08:46:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:46:58 : INFO : Creating the BED File.
08:47:06 : INFO : Saving Bed File as 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:47:07 : INFO : Execution Time = 0.16 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:47:07 : INFO : Running: touch /tmp/nxf.mXOV0Mklku/659_cTi-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok
08:47:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_cTi-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_cTi-T1-TRNA-1_B23MHV2LT4_1
[W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai