08:05:57 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[5650000], rate=13038461.54/min
[5660000], rate=13061538.46/min
[5670000], rate=13084615.38/min
[5680000], rate=13107692.31/min
[5690000], rate=12644444.44/min
[5700000], rate=12666666.67/min
[5710000], rate=12688888.89/min
[5720000], rate=12711111.11/min
[5730000], rate=12733333.33/min
[5740000], rate=12755555.56/min
[5750000], rate=12777777.78/min
[5760000], rate=12800000.00/min
[5770000], rate=12822222.22/min
[5780000], rate=12844444.44/min
[5790000], rate=12866666.67/min
[5800000], rate=12888888.89/min
[5810000], rate=12911111.11/min
[5820000], rate=12933333.33/min
[5830000], rate=12955555.56/min
[5840000], rate=12977777.78/min
[5850000], rate=13000000.00/min
[5860000], rate=13022222.22/min
[5870000], rate=13044444.44/min
[5880000], rate=13066666.67/min
[5890000], rate=13088888.89/min
[5900000], rate=13111111.11/min
[5910000], rate=13133333.33/min
[5920000], rate=12685714.29/min
[5930000], rate=12707142.86/min
[5940000], rate=12728571.43/min
[5950000], rate=12750000.00/min
[5960000], rate=12771428.57/min
[5970000], rate=12792857.14/min
[5980000], rate=12814285.71/min
[5990000], rate=12835714.29/min
[6000000], rate=12857142.86/min
[6010000], rate=12878571.43/min
[6020000], rate=12900000.00/min
[6030000], rate=12921428.57/min
[6040000], rate=12942857.14/min
[6050000], rate=12964285.71/min
[6060000], rate=12985714.29/min
[6070000], rate=13007142.86/min
[6080000], rate=13028571.43/min
[6090000], rate=13050000.00/min
[6100000], rate=13071428.57/min
[6110000], rate=13092857.14/min
[6120000], rate=13114285.71/min
[6130000], rate=13135714.29/min
[6140000], rate=12703448.28/min
[6150000], rate=12724137.93/min
[6160000], rate=12744827.59/min
[6170000], rate=12765517.24/min
[6180000], rate=12786206.90/min
[6190000], rate=12806896.55/min
[6200000], rate=12827586.21/min
[6210000], rate=12848275.86/min
[6220000], rate=12868965.52/min
[6230000], rate=12889655.17/min
[6240000], rate=12910344.83/min
[6250000], rate=12931034.48/min
[6260000], rate=12951724.14/min
[6270000], rate=12972413.79/min
[6280000], rate=12993103.45/min
[6290000], rate=13013793.10/min
[6300000], rate=13034482.76/min
[6310000], rate=13055172.41/min 08:06:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00703_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00703_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_00703_B23MVV7LT4_1.introns: identified 2873 cancer introns
08:06:34 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00703_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00703_B23MVV7LT4_1.cancer.introns.prelim
08:06:34 : INFO : Running: touch /tmp/nxf.YGR3Qefxdq/tih_rna_sample_00703_B23MVV7LT4_1.chckpts/prelim_introns.ok
08:06:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00703_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00703_B23MVV7LT4_1.cancer.introns
08:06:35 : 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_00703_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00703_B23MVV7LT4_1.cancer.introns
08:06:35 : INFO : Running: touch /tmp/nxf.YGR3Qefxdq/tih_rna_sample_00703_B23MVV7LT4_1.chckpts/introns_filtered.ok
08:06:35 : INFO : -found 1417 cancer introns
08:06:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00703_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00703_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00703_B23MVV7LT4_1.introns.for_IGV.bed
08:06:35 : INFO : Creating the BED File.
08:06:40 : INFO : Saving Bed File as tih_rna_sample_00703_B23MVV7LT4_1.introns.for_IGV.bed
08:06:40 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00703_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00703_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00703_B23MVV7LT4_1.introns.for_IGV.bed
08:06:40 : INFO : Running: touch /tmp/nxf.YGR3Qefxdq/tih_rna_sample_00703_B23MVV7LT4_1.chckpts/intron_igv_bed.ok
08:06:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00703_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00703_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00703_B23MVV7LT4_1
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00703_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
08:13:31 : INFO : Execution Time = 6.84 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00703_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00703_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00703_B23MVV7LT4_1
08:13:31 : INFO : Running: touch /tmp/nxf.YGR3Qefxdq/tih_rna_sample_00703_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok
08:13:31 : INFO : Running: samtools sort -o tih_rna_sample_00703_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00703_B23MVV7LT4_1.cancer_intron_reads.bam
08:13:31 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o tih_rna_sample_00703_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00703_B23MVV7LT4_1.cancer_intron_reads.bam
08:13:31 : INFO : Running: touch /tmp/nxf.YGR3Qefxdq/tih_rna_sample_00703_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok
08:13:31 : INFO : Running: samtools sort -o tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.bam
[bam_sort_core] merging from 34 files and 1 in-memory blocks...
08:20:46 : INFO : Execution Time = 7.24 minutes. CMD: samtools sort -o tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.bam
08:20:46 : INFO : Running: touch /tmp/nxf.YGR3Qefxdq/tih_rna_sample_00703_B23MVV7LT4_1.chckpts/sort_gene_reads.ok
08:20:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.bam
08:22:45 : INFO : Execution Time = 1.99 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.bam
08:22:45 : INFO : Running: touch /tmp/nxf.YGR3Qefxdq/tih_rna_sample_00703_B23MVV7LT4_1.chckpts/tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok
08:22:45 : INFO : Running: samtools sort -o tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
08:23:12 : INFO : Execution Time = 0.45 minutes. CMD: samtools sort -o tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp
08:23:12 : INFO : Running: touch /tmp/nxf.YGR3Qefxdq/tih_rna_sample_00703_B23MVV7LT4_1.chckpts/tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
08:23:12 : INFO : Running: samtools index tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.sifted.bam
08:23:16 : INFO : Execution Time = 0.05 minutes. CMD: samtools index tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.sifted.bam
08:23:16 : INFO : Running: touch /tmp/nxf.YGR3Qefxdq/tih_rna_sample_00703_B23MVV7LT4_1.chckpts/tih_rna_sample_00703_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok
08:23:16 : INFO : Running: samtools index tih_rna_sample_00703_B23MVV7LT4_1.cancer_intron_reads.sorted.bam
08:23:16 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00703_B23MVV7LT4_1.cancer_intron_reads.sorted.bam
08:23:16 : INFO : Running: touch /tmp/nxf.YGR3Qefxdq/tih_rna_sample_00703_B23MVV7LT4_1.chckpts/tih_rna_sample_00703_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok
08:23:16 : INFO : Running: create_report tih_rna_sample_00703_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00703_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00703_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00703_B23MVV7LT4_1'
08:27:35 : INFO : Execution Time = 4.33 minutes. CMD: create_report tih_rna_sample_00703_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00703_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00703_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00703_B23MVV7LT4_1'
08:27:35 : INFO : Running: touch /tmp/nxf.YGR3Qefxdq/tih_rna_sample_00703_B23MVV7LT4_1.chckpts/igv_create_html.ok
08:27:35 : INFO : done.