08:10:44 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [220000], rate=13200000.00/min [230000], rate=13800000.00/min [240000], rate=14400000.00/min [250000], rate=15000000.00/min [260000], rate=15600000.00/min [270000], rate=16200000.00/min [280000], rate=16800000.00/min [290000], rate=17400000.00/min [300000], rate=18000000.00/min [310000], rate=18600000.00/min [320000], rate=19200000.00/min [330000], rate=19800000.00/min [340000], rate=20400000.00/min [350000], rate=21000000.00/min [360000], rate=21600000.00/min [370000], rate=22200000.00/min [380000], rate=22800000.00/min [390000], rate=23400000.00/min [400000], rate=24000000.00/min [410000], rate=24600000.00/min [420000], rate=25200000.00/min [430000], rate=25800000.00/min [440000], rate=26400000.00/min [450000], rate=27000000.00/min [460000], rate=27600000.00/min [470000], rate=28200000.00/min [480000], rate=28800000.00/min [490000], rate=29400000.00/min [500000], rate=30000000.00/min [510000], rate=15300000.00/min [520000], rate=15600000.00/min [530000], rate=15900000.00/min [540000], rate=16200000.00/min [550000], rate=16500000.00/min [560000], rate=16800000.00/min [570000], rate=17100000.00/min [580000], rate=17400000.00/min [590000], rate=17700000.00/min [600000], rate=18000000.00/min [610000], rate=18300000.00/min [620000], rate=18600000.00/min [630000], rate=18900000.00/min [640000], rate=19200000.00/min [650000], rate=19500000.00/min [660000], rate=19800000.00/min [670000], rate=20100000.00/min [680000], rate=20400000.00/min [690000], rate=20700000.00/min [700000], rate=21000000.00/min [710000], rate=21300000.00/min [720000], rate=21600000.00/min [730000], rate=21900000.00/min [740000], rate=22200000.00/min [750000], rate=22500000.00/min [760000], rate=22800000.00/min [770000], rate=23100000.00/min [780000], rate=23400000.00/min [790000], rate=15800000.00/min [800000], rate=16000000.00/min [810000], rate=16200000.00/min [820000], 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[3930000], rate=16842857.14/min [3940000], rate=16885714.29/min [3950000], rate=16928571.43/min [3960000], rate=16971428.57/min [3970000], rate=17014285.71/min [3980000], rate=17057142.86/min [3990000], rate=17100000.00/min [4000000], rate=17142857.14/min [4010000], rate=17185714.29/min [4020000], rate=17228571.43/min [4030000], rate=17271428.57/min [4040000], rate=17314285.71/min [4050000], rate=17357142.86/min [4060000], rate=17400000.00/min [4070000], rate=17442857.14/min [4080000], rate=17485714.29/min [4090000], rate=17528571.43/min [4100000], rate=17571428.57/min [4110000], rate=17614285.71/min [4120000], rate=17657142.86/min [4130000], rate=17700000.00/min [4140000], rate=17742857.14/min [4150000], rate=17785714.29/min [4160000], rate=17828571.43/min [4170000], rate=16680000.00/min [4180000], rate=16720000.00/min [4190000], rate=16760000.00/min [4200000], rate=16800000.00/min [4210000], rate=16840000.00/min [4220000], rate=16880000.00/min [4230000], rate=16920000.00/min [4240000], rate=16960000.00/min [4250000], rate=17000000.00/min [4260000], rate=17040000.00/min [4270000], rate=17080000.00/min [4280000], rate=17120000.00/min [4290000], rate=17160000.00/min [4300000], rate=17200000.00/min [4310000], rate=17240000.00/min [4320000], rate=17280000.00/min [4330000], rate=17320000.00/min [4340000], rate=17360000.00/min [4350000], rate=17400000.00/min [4360000], rate=17440000.00/min [4370000], rate=17480000.00/min [4380000], rate=17520000.00/min [4390000], rate=17560000.00/min [4400000], rate=17600000.00/min [4410000], rate=17640000.00/min [4420000], rate=17680000.00/min [4430000], rate=17720000.00/min [4440000], rate=17760000.00/min [4450000], rate=17800000.00/min [4460000], rate=16725000.00/min [4470000], rate=16762500.00/min [4480000], rate=16800000.00/min [4490000], rate=16837500.00/min [4500000], rate=16875000.00/min [4510000], rate=16912500.00/min [4520000], rate=16950000.00/min [4530000], rate=16987500.00/min [4540000], rate=17025000.00/min [4550000], rate=17062500.00/min [4560000], rate=17100000.00/min [4570000], rate=17137500.00/min [4580000], rate=17175000.00/min [4590000], rate=17212500.00/min [4600000], rate=17250000.00/min [4610000], rate=17287500.00/min [4620000], rate=17325000.00/min [4630000], rate=17362500.00/min [4640000], rate=17400000.00/min [4650000], rate=17437500.00/min [4660000], rate=17475000.00/min [4670000], rate=17512500.00/min [4680000], rate=17550000.00/min [4690000], rate=17587500.00/min [4700000], rate=17625000.00/min [4710000], rate=17662500.00/min [4720000], rate=17700000.00/min [4730000], rate=17737500.00/min [4740000], rate=17775000.00/min [4750000], rate=17812500.00/min [4760000], rate=16800000.00/min [4770000], rate=16835294.12/min [4780000], rate=16870588.24/min [4790000], rate=16905882.35/min [4800000], rate=16941176.47/min [4810000], rate=16976470.59/min [4820000], rate=17011764.71/min [4830000], rate=17047058.82/min 08:11:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-8e3550-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-8e3550-R1_A23YTGFLT4_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-8e3550-R1_A23YTGFLT4_1.introns: identified 6272 cancer introns 08:11:07 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-8e3550-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer.introns.prelim 08:11:07 : INFO : Running: touch /tmp/nxf.RMfBdkVV3T/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 08:11:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer.introns 08:11:08 : 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-8e3550-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer.introns 08:11:08 : INFO : Running: touch /tmp/nxf.RMfBdkVV3T/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 08:11:08 : INFO : -found 1947 cancer introns 08:11:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-8e3550-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-8e3550-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:11:08 : INFO : Creating the BED File. 08:11:13 : INFO : Saving Bed File as aih-tih-sc-8e3550-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:11:13 : INFO : Execution Time = 0.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-8e3550-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-8e3550-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:11:13 : INFO : Running: touch /tmp/nxf.RMfBdkVV3T/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 08:11:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-8e3550-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-8e3550-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-8e3550-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 08:22:27 : INFO : Execution Time = 11.24 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-8e3550-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-8e3550-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1 08:22:27 : INFO : Running: touch /tmp/nxf.RMfBdkVV3T/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 08:22:27 : INFO : Running: samtools sort -o aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer_intron_reads.bam 08:22:28 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer_intron_reads.bam 08:22:28 : INFO : Running: touch /tmp/nxf.RMfBdkVV3T/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 08:22:28 : INFO : Running: samtools sort -o aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 50 files and 1 in-memory blocks... 08:36:08 : INFO : Execution Time = 13.66 minutes. CMD: samtools sort -o aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.bam 08:36:08 : INFO : Running: touch /tmp/nxf.RMfBdkVV3T/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok 08:36:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.bam 08:40:01 : INFO : Execution Time = 3.88 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.bam 08:40:01 : INFO : Running: touch /tmp/nxf.RMfBdkVV3T/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 08:40:01 : INFO : Running: samtools sort -o aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 2 files and 1 in-memory blocks... 08:40:47 : INFO : Execution Time = 0.77 minutes. CMD: samtools sort -o aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp 08:40:47 : INFO : Running: touch /tmp/nxf.RMfBdkVV3T/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 08:40:47 : INFO : Running: samtools index aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 08:40:52 : INFO : Execution Time = 0.08 minutes. CMD: samtools index aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 08:40:52 : INFO : Running: touch /tmp/nxf.RMfBdkVV3T/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 08:40:52 : INFO : Running: samtools index aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 08:40:52 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 08:40:52 : INFO : Running: touch /tmp/nxf.RMfBdkVV3T/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 08:40:52 : INFO : Running: create_report aih-tih-sc-8e3550-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-8e3550-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-8e3550-R1_A23YTGFLT4_1' 08:46:34 : INFO : Execution Time = 5.69 minutes. CMD: create_report aih-tih-sc-8e3550-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-8e3550-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-8e3550-R1_A23YTGFLT4_1' 08:46:34 : INFO : Running: touch /tmp/nxf.RMfBdkVV3T/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok 08:46:34 : INFO : done.