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rate=14750000.00/min [11810000], rate=14461224.49/min [11820000], rate=14473469.39/min [11830000], rate=14485714.29/min [11840000], rate=14497959.18/min [11850000], rate=14510204.08/min [11860000], rate=14522448.98/min [11870000], rate=14534693.88/min [11880000], rate=14546938.78/min [11890000], rate=14559183.67/min [11900000], rate=14571428.57/min [11910000], rate=14583673.47/min [11920000], rate=14595918.37/min [11930000], rate=14608163.27/min [11940000], rate=14620408.16/min [11950000], rate=14632653.06/min [11960000], rate=14644897.96/min [11970000], rate=14657142.86/min [11980000], rate=14669387.76/min [11990000], rate=14681632.65/min [12000000], rate=14693877.55/min [12010000], rate=14706122.45/min [12020000], rate=14718367.35/min [12030000], rate=14730612.24/min [12040000], rate=14742857.14/min [12050000], rate=14755102.04/min [12060000], rate=14767346.94/min [12070000], rate=14779591.84/min [12080000], rate=14791836.73/min [12090000], rate=14508000.00/min [12100000], rate=14520000.00/min [12110000], rate=14532000.00/min [12120000], rate=14544000.00/min [12130000], rate=14556000.00/min [12140000], rate=14568000.00/min [12150000], rate=14580000.00/min [12160000], rate=14592000.00/min [12170000], rate=14604000.00/min [12180000], rate=14616000.00/min [12190000], rate=14628000.00/min [12200000], rate=14640000.00/min [12210000], rate=14652000.00/min [12220000], rate=14664000.00/min [12230000], rate=14676000.00/min [12240000], rate=14688000.00/min [12250000], rate=14700000.00/min [12260000], rate=14712000.00/min [12270000], rate=14724000.00/min [12280000], rate=14736000.00/min [12290000], rate=14748000.00/min [12300000], rate=14760000.00/min [12310000], rate=14772000.00/min [12320000], rate=14784000.00/min [12330000], rate=14796000.00/min [12340000], rate=14808000.00/min [12350000], rate=14820000.00/min [12360000], rate=14541176.47/min [12370000], rate=14552941.18/min [12380000], rate=14564705.88/min [12390000], rate=14576470.59/min [12400000], rate=14588235.29/min [12410000], rate=14600000.00/min [12420000], rate=14611764.71/min [12430000], rate=14623529.41/min [12440000], rate=14635294.12/min [12450000], rate=14647058.82/min [12460000], rate=14658823.53/min [12470000], rate=14670588.24/min [12480000], rate=14682352.94/min [12490000], rate=14694117.65/min [12500000], rate=14705882.35/min [12510000], rate=14717647.06/min [12520000], rate=14729411.76/min [12530000], rate=14741176.47/min [12540000], rate=14752941.18/min [12550000], rate=14764705.88/min [12560000], rate=14776470.59/min [12570000], rate=14788235.29/min [12580000], rate=14800000.00/min [12590000], rate=14811764.71/min [12600000], rate=14823529.41/min [12610000], rate=14835294.12/min [12620000], rate=14847058.82/min [12630000], rate=14858823.53/min [12640000], rate=14584615.38/min [12650000], rate=14596153.85/min 09:31:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-884b4c-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-884b4c-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-884b4c-R1_B23WHYVLT4_1.introns: identified 5647 cancer introns 09:31:04 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-884b4c-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-884b4c-R1_B23WHYVLT4_1.cancer.introns.prelim 09:31:04 : INFO : Running: touch /tmp/nxf.fGtBR5R1xc/aih-tih-sc-884b4c-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok 09:31:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-884b4c-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-884b4c-R1_B23WHYVLT4_1.cancer.introns 09:31:05 : 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-884b4c-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-884b4c-R1_B23WHYVLT4_1.cancer.introns 09:31:05 : INFO : Running: touch /tmp/nxf.fGtBR5R1xc/aih-tih-sc-884b4c-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok 09:31:05 : INFO : -found 2712 cancer introns 09:31:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-884b4c-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-884b4c-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-884b4c-R1_B23WHYVLT4_1.introns.for_IGV.bed 09:31:05 : INFO : Creating the BED File. 09:31:12 : INFO : Saving Bed File as aih-tih-sc-884b4c-R1_B23WHYVLT4_1.introns.for_IGV.bed 09:31:12 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-884b4c-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-884b4c-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-884b4c-R1_B23WHYVLT4_1.introns.for_IGV.bed 09:31:12 : INFO : Running: touch /tmp/nxf.fGtBR5R1xc/aih-tih-sc-884b4c-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok 09:31:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-884b4c-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-884b4c-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-884b4c-R1_B23WHYVLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-884b4c-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai