20:22:59 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=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=9900000.00/min [340000], rate=10200000.00/min [350000], rate=10500000.00/min [360000], rate=10800000.00/min [370000], rate=11100000.00/min [380000], rate=11400000.00/min [390000], 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rate=12000000.00/min [3210000], rate=12037500.00/min [3220000], rate=12075000.00/min [3230000], rate=12112500.00/min [3240000], rate=12150000.00/min [3250000], rate=12187500.00/min [3260000], rate=12225000.00/min [3270000], rate=12262500.00/min [3280000], rate=12300000.00/min [3290000], rate=12337500.00/min [3300000], rate=12375000.00/min [3310000], rate=11682352.94/min [3320000], rate=11717647.06/min [3330000], rate=11752941.18/min [3340000], rate=11788235.29/min [3350000], rate=11823529.41/min [3360000], rate=11858823.53/min [3370000], rate=11894117.65/min [3380000], rate=11929411.76/min [3390000], rate=11964705.88/min [3400000], rate=12000000.00/min [3410000], rate=12035294.12/min [3420000], rate=12070588.24/min [3430000], rate=12105882.35/min [3440000], rate=12141176.47/min [3450000], rate=12176470.59/min [3460000], rate=12211764.71/min [3470000], rate=12247058.82/min [3480000], rate=12282352.94/min [3490000], rate=12317647.06/min [3500000], rate=12352941.18/min [3510000], rate=11700000.00/min [3520000], rate=11733333.33/min [3530000], rate=11766666.67/min [3540000], rate=11800000.00/min [3550000], rate=11833333.33/min [3560000], rate=11866666.67/min [3570000], rate=11900000.00/min [3580000], rate=11933333.33/min [3590000], rate=11966666.67/min [3600000], rate=12000000.00/min [3610000], rate=12033333.33/min [3620000], rate=12066666.67/min [3630000], rate=12100000.00/min [3640000], rate=12133333.33/min [3650000], rate=12166666.67/min [3660000], rate=12200000.00/min [3670000], rate=12233333.33/min [3680000], rate=12266666.67/min [3690000], rate=12300000.00/min [3700000], rate=12333333.33/min [3710000], rate=12366666.67/min [3720000], rate=12400000.00/min [3730000], rate=11778947.37/min [3740000], rate=11810526.32/min [3750000], rate=11842105.26/min [3760000], rate=11873684.21/min [3770000], rate=11905263.16/min [3780000], rate=11936842.11/min [3790000], rate=11968421.05/min [3800000], rate=12000000.00/min [3810000], rate=12031578.95/min [3820000], rate=12063157.89/min [3830000], rate=12094736.84/min [3840000], rate=12126315.79/min [3850000], rate=12157894.74/min [3860000], rate=12189473.68/min [3870000], rate=12221052.63/min [3880000], rate=12252631.58/min [3890000], rate=12284210.53/min [3900000], rate=12315789.47/min [3910000], rate=12347368.42/min [3920000], rate=12378947.37/min [3930000], rate=12410526.32/min [3940000], rate=12442105.26/min [3950000], rate=12473684.21/min [3960000], rate=12505263.16/min [3970000], rate=12536842.11/min [3980000], rate=12568421.05/min [3990000], rate=12600000.00/min [4000000], rate=12631578.95/min [4010000], rate=12663157.89/min [4020000], rate=12694736.84/min [4030000], rate=12726315.79/min [4040000], rate=12757894.74/min [4050000], rate=12789473.68/min [4060000], rate=12180000.00/min [4070000], rate=12210000.00/min [4080000], rate=12240000.00/min [4090000], rate=12270000.00/min [4100000], rate=12300000.00/min [4110000], rate=12330000.00/min [4120000], rate=12360000.00/min [4130000], rate=12390000.00/min [4140000], rate=12420000.00/min [4150000], rate=12450000.00/min [4160000], rate=12480000.00/min [4170000], rate=12510000.00/min [4180000], rate=12540000.00/min [4190000], rate=12570000.00/min [4200000], rate=12600000.00/min [4210000], rate=12630000.00/min [4220000], rate=12660000.00/min [4230000], rate=12690000.00/min [4240000], rate=12720000.00/min [4250000], rate=12750000.00/min [4260000], rate=12780000.00/min [4270000], rate=12810000.00/min [4280000], rate=12840000.00/min [4290000], rate=12870000.00/min [4300000], rate=12900000.00/min [4310000], rate=12930000.00/min [4320000], rate=12960000.00/min [4330000], rate=12371428.57/min [4340000], rate=12400000.00/min [4350000], rate=12428571.43/min [4360000], rate=12457142.86/min [4370000], rate=12485714.29/min [4380000], rate=12514285.71/min [4390000], rate=12542857.14/min [4400000], rate=12571428.57/min [4410000], rate=12600000.00/min [4420000], rate=12628571.43/min [4430000], rate=12657142.86/min [4440000], rate=12685714.29/min [4450000], rate=12714285.71/min [4460000], rate=12742857.14/min [4470000], rate=12771428.57/min [4480000], rate=12800000.00/min [4490000], rate=12828571.43/min [4500000], rate=12857142.86/min [4510000], rate=12885714.29/min [4520000], rate=12914285.71/min [4530000], rate=12942857.14/min [4540000], rate=12971428.57/min [4550000], rate=13000000.00/min [4560000], rate=13028571.43/min [4570000], rate=13057142.86/min [4580000], rate=13085714.29/min [4590000], rate=13114285.71/min [4600000], rate=13142857.14/min [4610000], rate=13171428.57/min [4620000], rate=13200000.00/min [4630000], rate=13228571.43/min [4640000], rate=13257142.86/min [4650000], rate=13285714.29/min [4660000], rate=13314285.71/min [4670000], rate=13342857.14/min [4680000], rate=12763636.36/min [4690000], rate=12790909.09/min [4700000], rate=12818181.82/min [4710000], rate=12845454.55/min [4720000], rate=12872727.27/min [4730000], rate=12900000.00/min [4740000], rate=12927272.73/min [4750000], rate=12954545.45/min [4760000], rate=12981818.18/min [4770000], rate=13009090.91/min [4780000], rate=13036363.64/min [4790000], rate=13063636.36/min [4800000], rate=13090909.09/min [4810000], rate=13118181.82/min [4820000], rate=13145454.55/min [4830000], rate=13172727.27/min [4840000], rate=13200000.00/min [4850000], rate=13227272.73/min [4860000], rate=13254545.45/min [4870000], rate=13281818.18/min [4880000], rate=13309090.91/min [4890000], rate=13336363.64/min 20:23:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_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. -HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns: identified 129 cancer introns 20:23:28 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns.prelim 20:23:28 : INFO : Running: touch /tmp/nxf.tiSgvfQhzS/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok 20:23:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns 20:23:29 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns 20:23:29 : INFO : Running: touch /tmp/nxf.tiSgvfQhzS/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok 20:23:29 : INFO : -found 89 cancer introns 20:23:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns --cancer_introns HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:23:29 : INFO : Creating the BED File. 20:23:30 : INFO : Saving Bed File as HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:23:30 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns --cancer_introns HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:23:30 : INFO : Running: touch /tmp/nxf.tiSgvfQhzS/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok 20:23:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1 [W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai 20:23:42 : INFO : Execution Time = 0.20 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1 20:23:42 : INFO : Running: touch /tmp/nxf.tiSgvfQhzS/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok 20:23:42 : INFO : Running: samtools sort -o HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam 20:23:42 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam 20:23:42 : INFO : Running: touch /tmp/nxf.tiSgvfQhzS/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok 20:23:42 : INFO : Running: samtools sort -o HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.bam 20:23:53 : INFO : Execution Time = 0.18 minutes. CMD: samtools sort -o HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.bam 20:23:53 : INFO : Running: touch /tmp/nxf.tiSgvfQhzS/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok 20:23:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 20:23:56 : INFO : Execution Time = 0.06 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 20:23:56 : INFO : Running: touch /tmp/nxf.tiSgvfQhzS/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 20:23:56 : INFO : Running: samtools sort -o HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp 20:23:57 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp 20:23:57 : INFO : Running: touch /tmp/nxf.tiSgvfQhzS/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 20:23:57 : INFO : Running: samtools index HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 20:23:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools index HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 20:23:58 : INFO : Running: touch /tmp/nxf.tiSgvfQhzS/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 20:23:58 : INFO : Running: samtools index HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 20:23:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools index HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 20:23:58 : INFO : Running: touch /tmp/nxf.tiSgvfQhzS/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 20:23:58 : INFO : Running: create_report HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1' 20:24:08 : INFO : Execution Time = 0.18 minutes. CMD: create_report HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1' 20:24:08 : INFO : Running: touch /tmp/nxf.tiSgvfQhzS/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok 20:24:08 : INFO : done.