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[10400000], rate=13000000.00/min [10410000], rate=13012500.00/min [10420000], rate=13025000.00/min [10430000], rate=13037500.00/min [10440000], rate=13050000.00/min [10450000], rate=13062500.00/min [10460000], rate=13075000.00/min [10470000], rate=13087500.00/min [10480000], rate=13100000.00/min [10490000], rate=13112500.00/min [10500000], rate=13125000.00/min [10510000], rate=13137500.00/min [10520000], rate=12881632.65/min [10530000], rate=12893877.55/min [10540000], rate=12906122.45/min [10550000], rate=12918367.35/min [10560000], rate=12930612.24/min [10570000], rate=12942857.14/min [10580000], rate=12955102.04/min [10590000], rate=12967346.94/min [10600000], rate=12979591.84/min [10610000], rate=12991836.73/min [10620000], rate=13004081.63/min [10630000], rate=13016326.53/min [10640000], rate=13028571.43/min [10650000], rate=13040816.33/min [10660000], rate=13053061.22/min [10670000], rate=13065306.12/min [10680000], rate=13077551.02/min [10690000], rate=13089795.92/min [10700000], rate=13102040.82/min [10710000], rate=13114285.71/min [10720000], rate=13126530.61/min [10730000], rate=13138775.51/min [10740000], rate=13151020.41/min [10750000], rate=13163265.31/min [10760000], rate=12912000.00/min [10770000], rate=12924000.00/min [10780000], rate=12936000.00/min [10790000], rate=12948000.00/min [10800000], rate=12960000.00/min [10810000], rate=12972000.00/min [10820000], rate=12984000.00/min [10830000], rate=12996000.00/min [10840000], rate=13008000.00/min [10850000], rate=13020000.00/min [10860000], rate=13032000.00/min [10870000], rate=13044000.00/min [10880000], rate=13056000.00/min [10890000], rate=13068000.00/min [10900000], rate=13080000.00/min [10910000], rate=13092000.00/min [10920000], rate=13104000.00/min [10930000], rate=13116000.00/min 09:41:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-2a5468-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-2a5468-R1_B23WHYVLT4_1.introns: identified 7877 cancer introns 09:41:14 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns.prelim 09:41:14 : INFO : Running: touch /tmp/nxf.ghw27TllkF/aih-tih-sc-2a5468-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok 09:41:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns 09:41:14 : 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-2a5468-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns 09:41:14 : INFO : Running: touch /tmp/nxf.ghw27TllkF/aih-tih-sc-2a5468-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok 09:41:14 : INFO : -found 3805 cancer introns 09:41:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns.for_IGV.bed 09:41:15 : INFO : Creating the BED File. 09:41:24 : INFO : Saving Bed File as aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns.for_IGV.bed 09:41:24 : INFO : Execution Time = 0.17 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns.for_IGV.bed 09:41:24 : INFO : Running: touch /tmp/nxf.ghw27TllkF/aih-tih-sc-2a5468-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok 09:41:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-2a5468-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-2a5468-R1_B23WHYVLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a5468-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai