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/ca/69e0650559c8521219d4068c8834be/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/c0541e2e8563e4fc548a06f1735039/659_dc8-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/69e0650559c8521219d4068c8834be/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/c0541e2e8563e4fc548a06f1735039/659_dc8-T1-TRNA-1_B23WHTKLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/8080431a079e715f2cbd78833cef77/659_dc8-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/c0541e2e8563e4fc548a06f1735039/659_dc8-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (7 inputs) 08:51:44 : INFO : -reading 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rate=18077419.35/min [9350000], rate=18096774.19/min [9360000], rate=18116129.03/min [9370000], rate=17568750.00/min [9380000], rate=17587500.00/min [9390000], rate=17606250.00/min [9400000], rate=17625000.00/min [9410000], rate=17643750.00/min [9420000], rate=17662500.00/min [9430000], rate=17681250.00/min [9440000], rate=17700000.00/min [9450000], rate=17718750.00/min [9460000], rate=17737500.00/min [9470000], rate=17756250.00/min [9480000], rate=17775000.00/min [9490000], rate=17793750.00/min [9500000], rate=17812500.00/min [9510000], rate=17831250.00/min [9520000], rate=17850000.00/min [9530000], rate=17868750.00/min [9540000], rate=17887500.00/min [9550000], rate=17906250.00/min [9560000], rate=17925000.00/min [9570000], rate=17943750.00/min [9580000], rate=17962500.00/min [9590000], rate=17981250.00/min [9600000], rate=18000000.00/min [9610000], rate=18018750.00/min [9620000], rate=18037500.00/min [9630000], rate=18056250.00/min 08:52:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_dc8-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_dc8-T1-TRNA-1_B23WHTKLT4_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_dc8-T1-TRNA-1_B23WHTKLT4_1.introns: identified 4102 cancer introns 08:52:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_dc8-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_dc8-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim 08:52:24 : INFO : Running: touch /tmp/nxf.e0eAVh4Jyx/659_dc8-T1-TRNA-1_B23WHTKLT4_1.chckpts/prelim_introns.ok 08:52:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_dc8-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_dc8-T1-TRNA-1_B23WHTKLT4_1.cancer.introns 08:52:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_dc8-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_dc8-T1-TRNA-1_B23WHTKLT4_1.cancer.introns 08:52:24 : INFO : Running: touch /tmp/nxf.e0eAVh4Jyx/659_dc8-T1-TRNA-1_B23WHTKLT4_1.chckpts/introns_filtered.ok 08:52:24 : INFO : -found 2833 cancer introns 08:52:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_dc8-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_dc8-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_dc8-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed 08:52:24 : INFO : Creating the BED File. 08:52:32 : INFO : Saving Bed File as 659_dc8-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed 08:52:32 : INFO : Execution Time = 0.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_dc8-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_dc8-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_dc8-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed 08:52:32 : INFO : Running: touch /tmp/nxf.e0eAVh4Jyx/659_dc8-T1-TRNA-1_B23WHTKLT4_1.chckpts/intron_igv_bed.ok 08:52:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_dc8-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_dc8-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_dc8-T1-TRNA-1_B23WHTKLT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_dc8-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai 09:13:27 : INFO : Execution Time = 20.91 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_dc8-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_dc8-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_dc8-T1-TRNA-1_B23WHTKLT4_1 09:13:27 : INFO : Running: touch /tmp/nxf.e0eAVh4Jyx/659_dc8-T1-TRNA-1_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok 09:13:27 : INFO : Running: samtools sort -o 659_dc8-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_dc8-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam 09:13:27 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_dc8-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_dc8-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam 09:13:27 : INFO : Running: touch /tmp/nxf.e0eAVh4Jyx/659_dc8-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok 09:13:27 : INFO : Running: samtools sort -o 659_dc8-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_dc8-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam [bam_sort_core] merging from 100 files and 1 in-memory blocks...