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[9170000], rate=10788235.29/min [9180000], rate=10800000.00/min [9190000], rate=10811764.71/min [9200000], rate=10823529.41/min [9210000], rate=10835294.12/min [9220000], rate=10638461.54/min [9230000], rate=10650000.00/min [9240000], rate=10661538.46/min [9250000], rate=10673076.92/min [9260000], rate=10684615.38/min [9270000], rate=10696153.85/min [9280000], rate=10707692.31/min [9290000], rate=10719230.77/min [9300000], rate=10730769.23/min [9310000], rate=10742307.69/min [9320000], rate=10753846.15/min [9330000], rate=10765384.62/min [9340000], rate=10776923.08/min [9350000], rate=10788461.54/min [9360000], rate=10800000.00/min [9370000], rate=10811538.46/min [9380000], rate=10823076.92/min [9390000], rate=10834615.38/min [9400000], rate=10846153.85/min [9410000], rate=10652830.19/min [9420000], rate=10664150.94/min [9430000], rate=10675471.70/min [9440000], rate=10686792.45/min [9450000], rate=10698113.21/min [9460000], rate=10709433.96/min [9470000], rate=10720754.72/min [9480000], rate=10732075.47/min [9490000], rate=10743396.23/min [9500000], rate=10754716.98/min [9510000], rate=10766037.74/min [9520000], rate=10777358.49/min [9530000], rate=10788679.25/min [9540000], rate=10800000.00/min [9550000], rate=10811320.75/min [9560000], rate=10822641.51/min [9570000], rate=10833962.26/min [9580000], rate=10845283.02/min [9590000], rate=10856603.77/min [9600000], rate=10867924.53/min [9610000], rate=10879245.28/min [9620000], rate=10688888.89/min [9630000], rate=10700000.00/min [9640000], rate=10711111.11/min 08:40:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bhK-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bhK-T1-TRNA-1_B23MHV2LT4_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. -659_bhK-T1-TRNA-1_B23MHV2LT4_1.introns: identified 6936 cancer introns 08:40:32 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bhK-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bhK-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 08:40:32 : INFO : Running: touch /tmp/nxf.8eTFisrw26/659_bhK-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 08:40:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bhK-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bhK-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:40:32 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bhK-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bhK-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:40:32 : INFO : Running: touch /tmp/nxf.8eTFisrw26/659_bhK-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 08:40:32 : INFO : -found 2002 cancer introns 08:40:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bhK-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bhK-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bhK-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:40:33 : INFO : Creating the BED File. 08:40:38 : INFO : Saving Bed File as 659_bhK-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:40:38 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bhK-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bhK-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bhK-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:40:38 : INFO : Running: touch /tmp/nxf.8eTFisrw26/659_bhK-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 08:40:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bhK-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bhK-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bhK-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai 09:04:52 : INFO : Execution Time = 24.22 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bhK-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bhK-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bhK-T1-TRNA-1_B23MHV2LT4_1 09:04:52 : INFO : Running: touch /tmp/nxf.8eTFisrw26/659_bhK-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok 09:04:52 : INFO : Running: samtools sort -o 659_bhK-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bhK-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:04:52 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_bhK-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bhK-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:04:52 : INFO : Running: touch /tmp/nxf.8eTFisrw26/659_bhK-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok 09:04:52 : INFO : Running: samtools sort -o 659_bhK-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_bhK-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam