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/1f/b81695631a2a1e1ea9d58feb5065c2/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/18b1decae41e9bc03974590c50c365/659_bGW-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/18b1decae41e9bc03974590c50c365/659_bGW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/18b1decae41e9bc03974590c50c365/659_bGW-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/3890fa91286a6918704a491051759f/659_bGW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/b81695631a2a1e1ea9d58feb5065c2/.command.run ==> STAGING COMPLETE (7 inputs) 08:41:18 : INFO : -reading 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rate=17454545.45/min [9610000], rate=17472727.27/min [9620000], rate=17490909.09/min [9630000], rate=17509090.91/min [9640000], rate=17527272.73/min [9650000], rate=17545454.55/min [9660000], rate=17563636.36/min [9670000], rate=17581818.18/min [9680000], rate=17600000.00/min [9690000], rate=17100000.00/min [9700000], rate=17117647.06/min [9710000], rate=17135294.12/min [9720000], rate=17152941.18/min [9730000], rate=17170588.24/min [9740000], rate=17188235.29/min [9750000], rate=17205882.35/min [9760000], rate=17223529.41/min [9770000], rate=17241176.47/min [9780000], rate=17258823.53/min [9790000], rate=17276470.59/min [9800000], rate=17294117.65/min [9810000], rate=17311764.71/min [9820000], rate=17329411.76/min [9830000], rate=17347058.82/min [9840000], rate=17364705.88/min [9850000], rate=17382352.94/min [9860000], rate=17400000.00/min [9870000], rate=17417647.06/min [9880000], rate=17435294.12/min [9890000], rate=17452941.18/min [9900000], rate=17470588.24/min [9910000], rate=17488235.29/min [9920000], rate=17505882.35/min [9930000], rate=17523529.41/min [9940000], rate=17541176.47/min [9950000], rate=17558823.53/min [9960000], rate=17576470.59/min 08:42:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bGW-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_bGW-T1-TRNA-1_B23MHV2LT4_1.introns: identified 7763 cancer introns 08:42:03 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 08:42:03 : INFO : Running: touch /tmp/nxf.QVVw1ZHmcX/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 08:42:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:42:04 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:42:04 : INFO : Running: touch /tmp/nxf.QVVw1ZHmcX/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 08:42:04 : INFO : -found 2630 cancer introns 08:42:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:42:04 : INFO : Creating the BED File. 08:42:09 : INFO : Saving Bed File as 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:42:09 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:42:09 : INFO : Running: touch /tmp/nxf.QVVw1ZHmcX/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 08:42:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bGW-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai 09:01:45 : INFO : Execution Time = 19.60 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bGW-T1-TRNA-1_B23MHV2LT4_1 09:01:45 : INFO : Running: touch /tmp/nxf.QVVw1ZHmcX/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok 09:01:45 : INFO : Running: samtools sort -o 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:01:45 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:01:45 : INFO : Running: touch /tmp/nxf.QVVw1ZHmcX/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok 09:01:46 : INFO : Running: samtools sort -o 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam