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rate=16200000.00/min [6490000], rate=16225000.00/min [6500000], rate=16250000.00/min [6510000], rate=15624000.00/min [6520000], rate=15648000.00/min [6530000], rate=15672000.00/min [6540000], rate=15696000.00/min [6550000], rate=15720000.00/min [6560000], rate=15744000.00/min [6570000], rate=15768000.00/min [6580000], rate=15792000.00/min [6590000], rate=15816000.00/min [6600000], rate=15840000.00/min [6610000], rate=15864000.00/min [6620000], rate=15888000.00/min [6630000], rate=15912000.00/min [6640000], rate=15936000.00/min [6650000], rate=15960000.00/min [6660000], rate=15984000.00/min [6670000], rate=16008000.00/min [6680000], rate=16032000.00/min [6690000], rate=16056000.00/min [6700000], rate=16080000.00/min [6710000], rate=16104000.00/min [6720000], rate=16128000.00/min [6730000], rate=16152000.00/min [6740000], rate=16176000.00/min [6750000], rate=16200000.00/min [6760000], rate=16224000.00/min [6770000], rate=16248000.00/min [6780000], rate=16272000.00/min [6790000], rate=16296000.00/min [6800000], rate=15692307.69/min [6810000], rate=15715384.62/min [6820000], rate=15738461.54/min [6830000], rate=15761538.46/min [6840000], rate=15784615.38/min [6850000], rate=15807692.31/min [6860000], rate=15830769.23/min [6870000], rate=15853846.15/min [6880000], rate=15876923.08/min [6890000], rate=15900000.00/min [6900000], rate=15923076.92/min [6910000], rate=15946153.85/min [6920000], rate=15969230.77/min [6930000], rate=15992307.69/min [6940000], rate=16015384.62/min [6950000], rate=16038461.54/min [6960000], rate=16061538.46/min [6970000], rate=16084615.38/min [6980000], rate=16107692.31/min [6990000], rate=16130769.23/min [7000000], rate=16153846.15/min [7010000], rate=16176923.08/min [7020000], rate=16200000.00/min [7030000], rate=16223076.92/min [7040000], rate=16246153.85/min [7050000], rate=15666666.67/min [7060000], rate=15688888.89/min [7070000], rate=15711111.11/min [7080000], rate=15733333.33/min [7090000], rate=15755555.56/min [7100000], rate=15777777.78/min [7110000], rate=15800000.00/min [7120000], rate=15822222.22/min [7130000], rate=15844444.44/min [7140000], rate=15866666.67/min [7150000], rate=15888888.89/min [7160000], rate=15911111.11/min [7170000], rate=15933333.33/min [7180000], rate=15955555.56/min [7190000], rate=15977777.78/min [7200000], rate=16000000.00/min [7210000], rate=16022222.22/min [7220000], rate=16044444.44/min [7230000], rate=16066666.67/min [7240000], rate=16088888.89/min [7250000], rate=16111111.11/min [7260000], rate=16133333.33/min [7270000], rate=16155555.56/min [7280000], rate=16177777.78/min [7290000], rate=16200000.00/min [7300000], rate=16222222.22/min [7310000], rate=16244444.44/min [7320000], rate=16266666.67/min [7330000], rate=15707142.86/min [7340000], rate=15728571.43/min [7350000], rate=15750000.00/min [7360000], rate=15771428.57/min [7370000], rate=15792857.14/min [7380000], rate=15814285.71/min [7390000], rate=15835714.29/min [7400000], rate=15857142.86/min [7410000], rate=15878571.43/min [7420000], rate=15900000.00/min [7430000], rate=15921428.57/min [7440000], rate=15942857.14/min [7450000], rate=15964285.71/min [7460000], rate=15985714.29/min [7470000], rate=16007142.86/min [7480000], rate=16028571.43/min [7490000], rate=16050000.00/min [7500000], rate=16071428.57/min [7510000], rate=16092857.14/min [7520000], rate=16114285.71/min [7530000], rate=16135714.29/min [7540000], rate=16157142.86/min [7550000], rate=16178571.43/min [7560000], rate=16200000.00/min [7570000], rate=15662068.97/min [7580000], rate=15682758.62/min [7590000], rate=15703448.28/min [7600000], rate=15724137.93/min [7610000], rate=15744827.59/min [7620000], rate=15765517.24/min [7630000], rate=15786206.90/min [7640000], rate=15806896.55/min [7650000], rate=15827586.21/min [7660000], rate=15848275.86/min [7670000], rate=15868965.52/min [7680000], rate=15889655.17/min [7690000], rate=15910344.83/min [7700000], rate=15931034.48/min [7710000], rate=15951724.14/min [7720000], rate=15972413.79/min [7730000], rate=15993103.45/min [7740000], rate=16013793.10/min [7750000], rate=16034482.76/min [7760000], rate=16055172.41/min [7770000], rate=16075862.07/min [7780000], rate=16096551.72/min [7790000], rate=16117241.38/min [7800000], rate=16137931.03/min [7810000], rate=16158620.69/min [7820000], rate=16179310.34/min [7830000], rate=16200000.00/min [7840000], rate=16220689.66/min [7850000], rate=16241379.31/min [7860000], rate=15720000.00/min [7870000], rate=15740000.00/min [7880000], rate=15760000.00/min [7890000], rate=15780000.00/min [7900000], rate=15800000.00/min [7910000], rate=15820000.00/min [7920000], rate=15840000.00/min 09:03:18 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00624_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00624_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_00624_B23MVV7LT4_1.introns: identified 6921 cancer introns 09:03:19 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00624_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00624_B23MVV7LT4_1.cancer.introns.prelim 09:03:19 : INFO : Running: touch /tmp/nxf.ksri60eXYD/tih_rna_sample_00624_B23MVV7LT4_1.chckpts/prelim_introns.ok 09:03:19 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00624_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00624_B23MVV7LT4_1.cancer.introns 09:03:19 : 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_00624_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00624_B23MVV7LT4_1.cancer.introns 09:03:19 : INFO : Running: touch /tmp/nxf.ksri60eXYD/tih_rna_sample_00624_B23MVV7LT4_1.chckpts/introns_filtered.ok 09:03:19 : INFO : -found 3327 cancer introns 09:03:19 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00624_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00624_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00624_B23MVV7LT4_1.introns.for_IGV.bed 09:03:19 : INFO : Creating the BED File. 09:03:26 : INFO : Saving Bed File as tih_rna_sample_00624_B23MVV7LT4_1.introns.for_IGV.bed 09:03:27 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00624_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00624_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00624_B23MVV7LT4_1.introns.for_IGV.bed 09:03:27 : INFO : Running: touch /tmp/nxf.ksri60eXYD/tih_rna_sample_00624_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 09:03:27 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00624_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00624_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00624_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00624_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 09:22:46 : INFO : Execution Time = 19.33 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00624_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00624_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00624_B23MVV7LT4_1 09:22:46 : INFO : Running: touch /tmp/nxf.ksri60eXYD/tih_rna_sample_00624_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 09:22:46 : INFO : Running: samtools sort -o tih_rna_sample_00624_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00624_B23MVV7LT4_1.cancer_intron_reads.bam 09:22:47 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00624_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00624_B23MVV7LT4_1.cancer_intron_reads.bam 09:22:47 : INFO : Running: touch /tmp/nxf.ksri60eXYD/tih_rna_sample_00624_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 09:22:47 : INFO : Running: samtools sort -o tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.bam [bam_sort_core] merging from 93 files and 1 in-memory blocks... 09:43:50 : INFO : Execution Time = 21.04 minutes. CMD: samtools sort -o tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.bam 09:43:50 : INFO : Running: touch /tmp/nxf.ksri60eXYD/tih_rna_sample_00624_B23MVV7LT4_1.chckpts/sort_gene_reads.ok 09:43:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.bam 09:50:00 : INFO : Execution Time = 6.18 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.bam 09:50:00 : INFO : Running: touch /tmp/nxf.ksri60eXYD/tih_rna_sample_00624_B23MVV7LT4_1.chckpts/tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:50:00 : INFO : Running: samtools sort -o tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 09:50:55 : INFO : Execution Time = 0.92 minutes. CMD: samtools sort -o tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp 09:50:55 : INFO : Running: touch /tmp/nxf.ksri60eXYD/tih_rna_sample_00624_B23MVV7LT4_1.chckpts/tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:50:55 : INFO : Running: samtools index tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 09:51:02 : INFO : Execution Time = 0.11 minutes. CMD: samtools index tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 09:51:02 : INFO : Running: touch /tmp/nxf.ksri60eXYD/tih_rna_sample_00624_B23MVV7LT4_1.chckpts/tih_rna_sample_00624_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:51:02 : INFO : Running: samtools index tih_rna_sample_00624_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 09:51:02 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00624_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 09:51:02 : INFO : Running: touch /tmp/nxf.ksri60eXYD/tih_rna_sample_00624_B23MVV7LT4_1.chckpts/tih_rna_sample_00624_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:51:02 : INFO : Running: create_report tih_rna_sample_00624_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00624_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00624_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00624_B23MVV7LT4_1' 09:58:03 : INFO : Execution Time = 7.01 minutes. CMD: create_report tih_rna_sample_00624_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00624_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00624_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00624_B23MVV7LT4_1' 09:58:03 : INFO : Running: touch /tmp/nxf.ksri60eXYD/tih_rna_sample_00624_B23MVV7LT4_1.chckpts/igv_create_html.ok 09:58:03 : INFO : done.