Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/fe18918ef216609b9fff766b21ceb7/aih-tih-sc-5ceb9a-R1_A23YTGFLT4_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/77/fe18918ef216609b9fff766b21ceb7/aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/44fa44f0407f63bb7083a6f564b246/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/fe18918ef216609b9fff766b21ceb7/aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/09602c4cdecd64129d7a0b0e875cb3/aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/44fa44f0407f63bb7083a6f564b246/.command.run ==> STAGING COMPLETE (7 inputs) 08:52:43 : INFO 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rate=13100000.00/min [6560000], rate=13120000.00/min [6570000], rate=13140000.00/min [6580000], rate=13160000.00/min [6590000], rate=13180000.00/min [6600000], rate=13200000.00/min [6610000], rate=13220000.00/min [6620000], rate=13240000.00/min [6630000], rate=13260000.00/min [6640000], rate=13280000.00/min [6650000], rate=13300000.00/min [6660000], rate=13320000.00/min [6670000], rate=13340000.00/min [6680000], rate=12929032.26/min [6690000], rate=12948387.10/min [6700000], rate=12967741.94/min [6710000], rate=12987096.77/min [6720000], rate=13006451.61/min [6730000], rate=13025806.45/min [6740000], rate=13045161.29/min [6750000], rate=13064516.13/min [6760000], rate=13083870.97/min [6770000], rate=13103225.81/min [6780000], rate=13122580.65/min [6790000], rate=13141935.48/min [6800000], rate=13161290.32/min [6810000], rate=13180645.16/min [6820000], rate=13200000.00/min [6830000], rate=13219354.84/min [6840000], rate=13238709.68/min [6850000], rate=13258064.52/min [6860000], rate=13277419.35/min [6870000], rate=13296774.19/min [6880000], rate=13316129.03/min [6890000], rate=12918750.00/min [6900000], rate=12937500.00/min [6910000], rate=12956250.00/min [6920000], rate=12975000.00/min [6930000], rate=12993750.00/min [6940000], rate=13012500.00/min [6950000], rate=13031250.00/min [6960000], rate=13050000.00/min [6970000], rate=13068750.00/min [6980000], rate=13087500.00/min [6990000], rate=13106250.00/min [7000000], rate=13125000.00/min [7010000], rate=13143750.00/min [7020000], rate=13162500.00/min [7030000], rate=13181250.00/min [7040000], rate=13200000.00/min [7050000], rate=13218750.00/min [7060000], rate=13237500.00/min [7070000], rate=13256250.00/min [7080000], rate=13275000.00/min [7090000], rate=13293750.00/min [7100000], rate=13312500.00/min [7110000], rate=13331250.00/min [7120000], rate=13350000.00/min [7130000], rate=13368750.00/min [7140000], rate=13387500.00/min [7150000], rate=13000000.00/min [7160000], rate=13018181.82/min [7170000], rate=13036363.64/min [7180000], rate=13054545.45/min [7190000], rate=13072727.27/min [7200000], rate=13090909.09/min [7210000], rate=13109090.91/min [7220000], rate=13127272.73/min [7230000], rate=13145454.55/min [7240000], rate=13163636.36/min [7250000], rate=13181818.18/min [7260000], rate=13200000.00/min [7270000], rate=13218181.82/min [7280000], rate=13236363.64/min [7290000], rate=13254545.45/min [7300000], rate=13272727.27/min [7310000], rate=13290909.09/min [7320000], rate=13309090.91/min [7330000], rate=13327272.73/min [7340000], rate=13345454.55/min [7350000], rate=13363636.36/min [7360000], rate=13381818.18/min [7370000], rate=13400000.00/min [7380000], rate=13418181.82/min [7390000], rate=13436363.64/min [7400000], rate=13454545.45/min [7410000], rate=13472727.27/min [7420000], rate=13094117.65/min [7430000], rate=13111764.71/min [7440000], rate=13129411.76/min [7450000], rate=13147058.82/min [7460000], rate=13164705.88/min [7470000], rate=13182352.94/min [7480000], rate=13200000.00/min [7490000], rate=13217647.06/min [7500000], rate=13235294.12/min [7510000], rate=13252941.18/min [7520000], rate=13270588.24/min [7530000], rate=13288235.29/min [7540000], rate=13305882.35/min [7550000], rate=13323529.41/min [7560000], rate=13341176.47/min [7570000], rate=13358823.53/min [7580000], rate=13376470.59/min [7590000], rate=13394117.65/min [7600000], rate=13411764.71/min [7610000], rate=13429411.76/min [7620000], rate=13447058.82/min [7630000], rate=13464705.88/min [7640000], rate=13482352.94/min [7650000], rate=13500000.00/min [7660000], rate=13517647.06/min [7670000], rate=13535294.12/min [7680000], rate=13552941.18/min [7690000], rate=13182857.14/min [7700000], rate=13200000.00/min [7710000], rate=13217142.86/min [7720000], rate=13234285.71/min [7730000], rate=13251428.57/min [7740000], rate=13268571.43/min [7750000], rate=13285714.29/min [7760000], rate=13302857.14/min [7770000], rate=13320000.00/min [7780000], rate=13337142.86/min [7790000], rate=13354285.71/min [7800000], rate=13371428.57/min [7810000], rate=13388571.43/min [7820000], rate=13405714.29/min [7830000], rate=13422857.14/min [7840000], rate=13440000.00/min [7850000], rate=13457142.86/min [7860000], rate=13474285.71/min [7870000], rate=13491428.57/min [7880000], rate=13508571.43/min [7890000], rate=13525714.29/min [7900000], rate=13542857.14/min [7910000], rate=13560000.00/min [7920000], rate=13577142.86/min [7930000], rate=13594285.71/min [7940000], rate=13611428.57/min [7950000], rate=13628571.43/min 08:53:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-5ceb9a-R1_A23YTGFLT4_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-5ceb9a-R1_A23YTGFLT4_1.introns: identified 7456 cancer introns 08:53:30 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.cancer.introns.prelim 08:53:30 : INFO : Running: touch /tmp/nxf.hCsh0O08Qe/aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 08:53:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.cancer.introns 08:53:31 : 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-5ceb9a-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.cancer.introns 08:53:31 : INFO : Running: touch /tmp/nxf.hCsh0O08Qe/aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 08:53:31 : INFO : -found 2747 cancer introns 08:53:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:53:31 : INFO : Creating the BED File. 08:53:36 : INFO : Saving Bed File as aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:53:37 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:53:37 : INFO : Running: touch /tmp/nxf.hCsh0O08Qe/aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 08:53:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 09:13:02 : INFO : Execution Time = 19.43 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1 09:13:02 : INFO : Running: touch /tmp/nxf.hCsh0O08Qe/aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 09:13:02 : INFO : Running: samtools sort -o aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:13:03 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:13:03 : INFO : Running: touch /tmp/nxf.hCsh0O08Qe/aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 09:13:03 : INFO : Running: samtools sort -o aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.gene_reads.bam