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/c3/b5840c5068e983644bdb543835f7fd/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/78e926b96b2588440f4adffc6a8a11/aih-tih-sc-522d83-R1_B23WHYVLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/76a219fa3c219c28e8f2a24bf70351/aih-tih-sc-522d83-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/b5840c5068e983644bdb543835f7fd/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/78e926b96b2588440f4adffc6a8a11/aih-tih-sc-522d83-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/78e926b96b2588440f4adffc6a8a11/aih-tih-sc-522d83-R1_B23WHYVLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (7 inputs) 08:52:44 : INFO 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[10340000], rate=21393103.45/min [10350000], rate=21413793.10/min [10360000], rate=21434482.76/min [10370000], rate=21455172.41/min [10380000], rate=21475862.07/min [10390000], rate=21496551.72/min [10400000], rate=21517241.38/min [10410000], rate=21537931.03/min [10420000], rate=21558620.69/min [10430000], rate=21579310.34/min [10440000], rate=21600000.00/min [10450000], rate=21620689.66/min [10460000], rate=21641379.31/min [10470000], rate=21662068.97/min [10480000], rate=21682758.62/min [10490000], rate=21703448.28/min [10500000], rate=21724137.93/min [10510000], rate=21744827.59/min [10520000], rate=21765517.24/min [10530000], rate=21786206.90/min [10540000], rate=21806896.55/min [10550000], rate=21827586.21/min [10560000], rate=21848275.86/min [10570000], rate=21868965.52/min [10580000], rate=21889655.17/min [10590000], rate=21910344.83/min [10600000], rate=21200000.00/min [10610000], rate=21220000.00/min [10620000], rate=21240000.00/min [10630000], rate=21260000.00/min [10640000], rate=21280000.00/min [10650000], rate=21300000.00/min [10660000], rate=21320000.00/min [10670000], rate=21340000.00/min [10680000], rate=21360000.00/min [10690000], rate=21380000.00/min [10700000], rate=21400000.00/min [10710000], rate=21420000.00/min [10720000], rate=21440000.00/min [10730000], rate=21460000.00/min [10740000], rate=21480000.00/min [10750000], rate=21500000.00/min [10760000], rate=21520000.00/min [10770000], rate=21540000.00/min [10780000], rate=21560000.00/min [10790000], rate=21580000.00/min [10800000], rate=21600000.00/min [10810000], rate=21620000.00/min [10820000], rate=21640000.00/min [10830000], rate=21660000.00/min [10840000], rate=21680000.00/min [10850000], rate=21700000.00/min [10860000], rate=21720000.00/min [10870000], rate=21740000.00/min [10880000], rate=21760000.00/min [10890000], rate=21780000.00/min [10900000], rate=21800000.00/min [10910000], rate=21820000.00/min [10920000], rate=21840000.00/min [10930000], rate=21860000.00/min [10940000], rate=21880000.00/min [10950000], rate=21900000.00/min [10960000], rate=21920000.00/min [10970000], rate=21940000.00/min [10980000], rate=21960000.00/min [10990000], rate=21980000.00/min [11000000], rate=21290322.58/min 08:53:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-522d83-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-522d83-R1_B23WHYVLT4_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. -aih-tih-sc-522d83-R1_B23WHYVLT4_1.introns: identified 7499 cancer introns 08:53:23 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-522d83-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-522d83-R1_B23WHYVLT4_1.cancer.introns.prelim 08:53:23 : INFO : Running: touch /tmp/nxf.3DSbuDge4Z/aih-tih-sc-522d83-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok 08:53:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-522d83-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-522d83-R1_B23WHYVLT4_1.cancer.introns 08:53:24 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-522d83-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-522d83-R1_B23WHYVLT4_1.cancer.introns 08:53:24 : INFO : Running: touch /tmp/nxf.3DSbuDge4Z/aih-tih-sc-522d83-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok 08:53:24 : INFO : -found 3136 cancer introns 08:53:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-522d83-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-522d83-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-522d83-R1_B23WHYVLT4_1.introns.for_IGV.bed 08:53:24 : INFO : Creating the BED File. 08:53:30 : INFO : Saving Bed File as aih-tih-sc-522d83-R1_B23WHYVLT4_1.introns.for_IGV.bed 08:53:30 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-522d83-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-522d83-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-522d83-R1_B23WHYVLT4_1.introns.for_IGV.bed 08:53:30 : INFO : Running: touch /tmp/nxf.3DSbuDge4Z/aih-tih-sc-522d83-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok 08:53:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-522d83-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-522d83-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-522d83-R1_B23WHYVLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-522d83-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai 09:12:47 : INFO : Execution Time = 19.28 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-522d83-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-522d83-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-522d83-R1_B23WHYVLT4_1 09:12:47 : INFO : Running: touch /tmp/nxf.3DSbuDge4Z/aih-tih-sc-522d83-R1_B23WHYVLT4_1.chckpts/reads_alignments_extracted.ok 09:12:47 : INFO : Running: samtools sort -o aih-tih-sc-522d83-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-522d83-R1_B23WHYVLT4_1.cancer_intron_reads.bam 09:12:47 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-522d83-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-522d83-R1_B23WHYVLT4_1.cancer_intron_reads.bam 09:12:47 : INFO : Running: touch /tmp/nxf.3DSbuDge4Z/aih-tih-sc-522d83-R1_B23WHYVLT4_1.chckpts/sort_cancer_intron_reads.ok 09:12:47 : INFO : Running: samtools sort -o aih-tih-sc-522d83-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-522d83-R1_B23WHYVLT4_1.gene_reads.bam