07:55:31 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [20000], rate=1200000.00/min [30000], rate=1800000.00/min [40000], rate=2400000.00/min [50000], rate=3000000.00/min [60000], rate=3600000.00/min [70000], rate=4200000.00/min [80000], rate=4800000.00/min [90000], rate=5400000.00/min [100000], rate=6000000.00/min [110000], rate=6600000.00/min [120000], rate=7200000.00/min [130000], rate=7800000.00/min [140000], rate=8400000.00/min [150000], rate=9000000.00/min [160000], rate=9600000.00/min [170000], rate=10200000.00/min [180000], rate=10800000.00/min [190000], rate=11400000.00/min [200000], rate=12000000.00/min [210000], rate=12600000.00/min [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=8100000.00/min [280000], rate=8400000.00/min [290000], rate=8700000.00/min [300000], rate=9000000.00/min [310000], 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rate=17150000.00/min [3440000], rate=17200000.00/min [3450000], rate=17250000.00/min [3460000], rate=17300000.00/min [3470000], rate=16015384.62/min [3480000], rate=16061538.46/min [3490000], rate=16107692.31/min [3500000], rate=16153846.15/min [3510000], rate=16200000.00/min [3520000], rate=16246153.85/min [3530000], rate=16292307.69/min [3540000], rate=16338461.54/min [3550000], rate=16384615.38/min [3560000], rate=16430769.23/min [3570000], rate=16476923.08/min [3580000], rate=16523076.92/min [3590000], rate=16569230.77/min [3600000], rate=16615384.62/min [3610000], rate=16661538.46/min [3620000], rate=16707692.31/min [3630000], rate=16753846.15/min [3640000], rate=16800000.00/min [3650000], rate=16846153.85/min [3660000], rate=16892307.69/min [3670000], rate=16938461.54/min [3680000], rate=16984615.38/min [3690000], rate=15814285.71/min [3700000], rate=15857142.86/min [3710000], rate=15900000.00/min [3720000], rate=15942857.14/min [3730000], rate=15985714.29/min [3740000], rate=16028571.43/min [3750000], rate=16071428.57/min [3760000], rate=16114285.71/min [3770000], rate=16157142.86/min [3780000], rate=16200000.00/min [3790000], rate=16242857.14/min [3800000], rate=16285714.29/min [3810000], rate=16328571.43/min [3820000], rate=16371428.57/min [3830000], rate=16414285.71/min [3840000], rate=16457142.86/min [3850000], rate=16500000.00/min [3860000], rate=16542857.14/min [3870000], rate=16585714.29/min [3880000], rate=16628571.43/min [3890000], rate=16671428.57/min [3900000], rate=16714285.71/min [3910000], rate=15640000.00/min [3920000], rate=15680000.00/min [3930000], rate=15720000.00/min [3940000], rate=15760000.00/min [3950000], rate=15800000.00/min [3960000], rate=15840000.00/min [3970000], rate=15880000.00/min [3980000], rate=15920000.00/min [3990000], rate=15960000.00/min [4000000], rate=16000000.00/min [4010000], rate=16040000.00/min [4020000], rate=16080000.00/min [4030000], rate=16120000.00/min [4040000], rate=16160000.00/min [4050000], rate=16200000.00/min [4060000], rate=16240000.00/min [4070000], rate=16280000.00/min [4080000], rate=16320000.00/min [4090000], rate=16360000.00/min [4100000], rate=16400000.00/min [4110000], rate=16440000.00/min [4120000], rate=16480000.00/min [4130000], rate=15487500.00/min [4140000], rate=15525000.00/min [4150000], rate=15562500.00/min [4160000], rate=15600000.00/min [4170000], rate=15637500.00/min [4180000], rate=15675000.00/min [4190000], rate=15712500.00/min [4200000], rate=15750000.00/min [4210000], rate=15787500.00/min [4220000], rate=15825000.00/min [4230000], rate=15862500.00/min [4240000], rate=15900000.00/min [4250000], rate=15937500.00/min [4260000], rate=15975000.00/min [4270000], rate=16012500.00/min [4280000], rate=16050000.00/min [4290000], rate=16087500.00/min [4300000], rate=16125000.00/min [4310000], rate=16162500.00/min [4320000], rate=16200000.00/min [4330000], rate=16237500.00/min [4340000], rate=16275000.00/min [4350000], rate=16312500.00/min [4360000], rate=15388235.29/min [4370000], rate=15423529.41/min [4380000], rate=15458823.53/min [4390000], rate=15494117.65/min [4400000], rate=15529411.76/min [4410000], rate=15564705.88/min [4420000], rate=15600000.00/min [4430000], rate=15635294.12/min [4440000], rate=15670588.24/min [4450000], rate=15705882.35/min [4460000], rate=15741176.47/min [4470000], rate=15776470.59/min [4480000], rate=15811764.71/min [4490000], rate=15847058.82/min [4500000], rate=15882352.94/min [4510000], rate=15917647.06/min [4520000], rate=15952941.18/min [4530000], rate=15988235.29/min [4540000], rate=16023529.41/min [4550000], rate=16058823.53/min [4560000], rate=16094117.65/min [4570000], rate=15233333.33/min [4580000], rate=15266666.67/min [4590000], rate=15300000.00/min [4600000], rate=15333333.33/min [4610000], rate=15366666.67/min [4620000], rate=15400000.00/min [4630000], rate=15433333.33/min [4640000], rate=15466666.67/min [4650000], rate=15500000.00/min [4660000], rate=15533333.33/min [4670000], rate=15566666.67/min [4680000], rate=15600000.00/min 07:55:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1.introns: identified 1792 cancer introns 07:55:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer.introns.prelim 07:55:57 : INFO : Running: touch /tmp/nxf.GejV6POI5t/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok 07:55:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer.introns 07:55:58 : 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-20b7e4-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer.introns 07:55:58 : INFO : Running: touch /tmp/nxf.GejV6POI5t/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok 07:55:58 : INFO : -found 933 cancer introns 07:55:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.introns.for_IGV.bed 07:55:58 : INFO : Creating the BED File. 07:56:02 : INFO : Saving Bed File as aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.introns.for_IGV.bed 07:56:02 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.introns.for_IGV.bed 07:56:02 : INFO : Running: touch /tmp/nxf.GejV6POI5t/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok 07:56:02 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-20b7e4-R1_B23WHYVLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai 08:03:10 : INFO : Execution Time = 7.13 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-20b7e4-R1_B23WHYVLT4_1 08:03:10 : INFO : Running: touch /tmp/nxf.GejV6POI5t/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.chckpts/reads_alignments_extracted.ok 08:03:10 : INFO : Running: samtools sort -o aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer_intron_reads.bam 08:03:10 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer_intron_reads.bam 08:03:10 : INFO : Running: touch /tmp/nxf.GejV6POI5t/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.chckpts/sort_cancer_intron_reads.ok 08:03:10 : INFO : Running: samtools sort -o aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.bam [bam_sort_core] merging from 28 files and 1 in-memory blocks... 08:10:40 : INFO : Execution Time = 7.49 minutes. CMD: samtools sort -o aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.bam 08:10:40 : INFO : Running: touch /tmp/nxf.GejV6POI5t/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.chckpts/sort_gene_reads.ok 08:10:40 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.bam 08:12:59 : INFO : Execution Time = 2.33 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.bam 08:12:59 : INFO : Running: touch /tmp/nxf.GejV6POI5t/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 08:12:59 : INFO : Running: samtools sort -o aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 1 files and 1 in-memory blocks... 08:13:28 : INFO : Execution Time = 0.48 minutes. CMD: samtools sort -o aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp 08:13:28 : INFO : Running: touch /tmp/nxf.GejV6POI5t/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 08:13:28 : INFO : Running: samtools index aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam 08:13:32 : INFO : Execution Time = 0.06 minutes. CMD: samtools index aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam 08:13:32 : INFO : Running: touch /tmp/nxf.GejV6POI5t/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 08:13:32 : INFO : Running: samtools index aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam 08:13:32 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam 08:13:32 : INFO : Running: touch /tmp/nxf.GejV6POI5t/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 08:13:32 : INFO : Running: create_report aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1' 08:18:06 : INFO : Execution Time = 4.57 minutes. CMD: create_report aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1' 08:18:06 : INFO : Running: touch /tmp/nxf.GejV6POI5t/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.chckpts/igv_create_html.ok 08:18:06 : INFO : done.