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/1e/ccbcbd1a18e9d3a8144f63e6d7c5c4/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/3b10bd4a02263bbc6b8ac4e3144907/aih-tih-sc-8a623b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/3b10bd4a02263bbc6b8ac4e3144907/aih-tih-sc-8a623b-R1_B23WHYVLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/3b10bd4a02263bbc6b8ac4e3144907/aih-tih-sc-8a623b-R1_B23WHYVLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/7fdb0c28d0833922beec3a3476a399/aih-tih-sc-8a623b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/ccbcbd1a18e9d3a8144f63e6d7c5c4/.command.run ==> STAGING COMPLETE (7 inputs) 09:22:13 : INFO 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[9740000], rate=14984615.38/min [9750000], rate=15000000.00/min [9760000], rate=15015384.62/min [9770000], rate=15030769.23/min [9780000], rate=15046153.85/min [9790000], rate=15061538.46/min [9800000], rate=15076923.08/min [9810000], rate=15092307.69/min [9820000], rate=15107692.31/min [9830000], rate=15123076.92/min [9840000], rate=14760000.00/min [9850000], rate=14775000.00/min [9860000], rate=14790000.00/min [9870000], rate=14805000.00/min [9880000], rate=14820000.00/min [9890000], rate=14835000.00/min [9900000], rate=14850000.00/min [9910000], rate=14865000.00/min [9920000], rate=14880000.00/min [9930000], rate=14895000.00/min [9940000], rate=14910000.00/min [9950000], rate=14925000.00/min [9960000], rate=14940000.00/min [9970000], rate=14955000.00/min [9980000], rate=14970000.00/min [9990000], rate=14985000.00/min [10000000], rate=15000000.00/min [10010000], rate=15015000.00/min [10020000], rate=15030000.00/min [10030000], rate=15045000.00/min [10040000], rate=15060000.00/min [10050000], rate=15075000.00/min [10060000], rate=15090000.00/min [10070000], rate=15105000.00/min [10080000], rate=15120000.00/min [10090000], rate=15135000.00/min [10100000], rate=15150000.00/min [10110000], rate=15165000.00/min [10120000], rate=15180000.00/min [10130000], rate=15195000.00/min [10140000], rate=14839024.39/min [10150000], rate=14853658.54/min [10160000], rate=14868292.68/min [10170000], rate=14882926.83/min [10180000], rate=14897560.98/min [10190000], rate=14912195.12/min [10200000], rate=14926829.27/min [10210000], rate=14941463.41/min [10220000], rate=14956097.56/min [10230000], rate=14970731.71/min [10240000], rate=14985365.85/min [10250000], rate=15000000.00/min [10260000], rate=15014634.15/min [10270000], rate=15029268.29/min [10280000], rate=15043902.44/min [10290000], rate=15058536.59/min [10300000], rate=15073170.73/min 09:23:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-8a623b-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-8a623b-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-8a623b-R1_B23WHYVLT4_1.introns: identified 6479 cancer introns 09:23:04 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-8a623b-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-8a623b-R1_B23WHYVLT4_1.cancer.introns.prelim 09:23:04 : INFO : Running: touch /tmp/nxf.ou5IEB6ZFL/aih-tih-sc-8a623b-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok 09:23:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-8a623b-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-8a623b-R1_B23WHYVLT4_1.cancer.introns 09:23:04 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-8a623b-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-8a623b-R1_B23WHYVLT4_1.cancer.introns 09:23:04 : INFO : Running: touch /tmp/nxf.ou5IEB6ZFL/aih-tih-sc-8a623b-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok 09:23:04 : INFO : -found 2740 cancer introns 09:23:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-8a623b-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-8a623b-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-8a623b-R1_B23WHYVLT4_1.introns.for_IGV.bed 09:23:05 : INFO : Creating the BED File. 09:23:11 : INFO : Saving Bed File as aih-tih-sc-8a623b-R1_B23WHYVLT4_1.introns.for_IGV.bed 09:23:11 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-8a623b-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-8a623b-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-8a623b-R1_B23WHYVLT4_1.introns.for_IGV.bed 09:23:11 : INFO : Running: touch /tmp/nxf.ou5IEB6ZFL/aih-tih-sc-8a623b-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok 09:23:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-8a623b-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-8a623b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-8a623b-R1_B23WHYVLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-8a623b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai