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rate=19244444.44/min [8670000], rate=19266666.67/min [8680000], rate=19288888.89/min [8690000], rate=19311111.11/min [8700000], rate=19333333.33/min [8710000], rate=19355555.56/min [8720000], rate=19377777.78/min [8730000], rate=19400000.00/min [8740000], rate=19422222.22/min [8750000], rate=19444444.44/min [8760000], rate=19466666.67/min [8770000], rate=19488888.89/min [8780000], rate=19511111.11/min [8790000], rate=19533333.33/min [8800000], rate=19555555.56/min [8810000], rate=18878571.43/min [8820000], rate=18900000.00/min [8830000], rate=18921428.57/min [8840000], rate=18942857.14/min [8850000], rate=18964285.71/min [8860000], rate=18985714.29/min [8870000], rate=19007142.86/min [8880000], rate=19028571.43/min [8890000], rate=19050000.00/min [8900000], rate=19071428.57/min [8910000], rate=19092857.14/min [8920000], rate=19114285.71/min [8930000], rate=19135714.29/min [8940000], rate=19157142.86/min [8950000], rate=19178571.43/min [8960000], rate=19200000.00/min [8970000], rate=19221428.57/min [8980000], rate=19242857.14/min [8990000], rate=19264285.71/min [9000000], rate=19285714.29/min [9010000], rate=19307142.86/min [9020000], rate=19328571.43/min [9030000], rate=19350000.00/min [9040000], rate=19371428.57/min [9050000], rate=19392857.14/min [9060000], rate=19414285.71/min [9070000], rate=19435714.29/min [9080000], rate=19457142.86/min [9090000], rate=19478571.43/min [9100000], rate=19500000.00/min [9110000], rate=19521428.57/min [9120000], rate=19542857.14/min [9130000], rate=19564285.71/min [9140000], rate=19585714.29/min [9150000], rate=19607142.86/min [9160000], rate=18951724.14/min [9170000], rate=18972413.79/min [9180000], rate=18993103.45/min [9190000], rate=19013793.10/min [9200000], rate=19034482.76/min [9210000], rate=19055172.41/min [9220000], rate=19075862.07/min [9230000], rate=19096551.72/min [9240000], rate=19117241.38/min [9250000], rate=19137931.03/min [9260000], rate=19158620.69/min [9270000], rate=19179310.34/min [9280000], rate=19200000.00/min [9290000], rate=19220689.66/min [9300000], rate=19241379.31/min [9310000], rate=19262068.97/min [9320000], rate=19282758.62/min [9330000], rate=19303448.28/min [9340000], rate=19324137.93/min [9350000], rate=19344827.59/min [9360000], rate=19365517.24/min [9370000], rate=19386206.90/min [9380000], rate=19406896.55/min [9390000], rate=19427586.21/min [9400000], rate=19448275.86/min [9410000], rate=19468965.52/min [9420000], rate=19489655.17/min [9430000], rate=19510344.83/min [9440000], rate=19531034.48/min [9450000], rate=19551724.14/min [9460000], rate=19572413.79/min [9470000], rate=19593103.45/min [9480000], rate=19613793.10/min [9490000], rate=19634482.76/min [9500000], rate=19655172.41/min [9510000], rate=19675862.07/min [9520000], rate=19040000.00/min [9530000], rate=19060000.00/min [9540000], rate=19080000.00/min [9550000], rate=19100000.00/min [9560000], rate=19120000.00/min [9570000], rate=19140000.00/min [9580000], rate=19160000.00/min [9590000], rate=19180000.00/min [9600000], rate=19200000.00/min [9610000], rate=19220000.00/min [9620000], rate=19240000.00/min [9630000], rate=19260000.00/min [9640000], rate=19280000.00/min 08:40:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00762_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00762_B23MVV7LT4_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. -tih_rna_sample_00762_B23MVV7LT4_1.introns: identified 8530 cancer introns 08:40:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00762_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns.prelim 08:40:44 : INFO : Running: touch /tmp/nxf.y0VhFUgJOH/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/prelim_introns.ok 08:40:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns 08:40:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns 08:40:44 : INFO : Running: touch /tmp/nxf.y0VhFUgJOH/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/introns_filtered.ok 08:40:44 : INFO : -found 3965 cancer introns 08:40:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00762_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed 08:40:44 : INFO : Creating the BED File. 08:40:51 : INFO : Saving Bed File as tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed 08:40:51 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00762_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00762_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed 08:40:51 : INFO : Running: touch /tmp/nxf.y0VhFUgJOH/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 08:40:52 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00762_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00762_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00762_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 09:02:00 : INFO : Execution Time = 21.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00762_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00762_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00762_B23MVV7LT4_1 09:02:00 : INFO : Running: touch /tmp/nxf.y0VhFUgJOH/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 09:02:00 : INFO : Running: samtools sort -o tih_rna_sample_00762_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00762_B23MVV7LT4_1.cancer_intron_reads.bam 09:02:01 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00762_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00762_B23MVV7LT4_1.cancer_intron_reads.bam 09:02:01 : INFO : Running: touch /tmp/nxf.y0VhFUgJOH/tih_rna_sample_00762_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 09:02:01 : INFO : Running: samtools sort -o tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00762_B23MVV7LT4_1.gene_reads.bam