07:30:27 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=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=15000000.00/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=15600000.00/min [790000], rate=15800000.00/min [800000], rate=16000000.00/min [810000], rate=16200000.00/min [820000], rate=16400000.00/min [830000], rate=16600000.00/min [840000], rate=16800000.00/min [850000], rate=17000000.00/min [860000], rate=17200000.00/min [870000], rate=17400000.00/min [880000], rate=17600000.00/min 07:30:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_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. -1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 203 cancer introns 07:30:34 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim 07:30:34 : INFO : Running: touch /tmp/nxf.wdl5ZbFxwU/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok 07:30:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 07:30:35 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 07:30:35 : INFO : Running: touch /tmp/nxf.wdl5ZbFxwU/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok 07:30:35 : INFO : -found 119 cancer introns 07:30:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 07:30:35 : INFO : Creating the BED File. 07:30:36 : INFO : Saving Bed File as 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 07:30:36 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 07:30:36 : INFO : Running: touch /tmp/nxf.wdl5ZbFxwU/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok 07:30:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1 [W::hts_idx_load3] The index file is older than the data file: 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai 07:30:43 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1 07:30:43 : INFO : Running: touch /tmp/nxf.wdl5ZbFxwU/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok 07:30:43 : INFO : Running: samtools sort -o 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 07:30:43 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 07:30:43 : INFO : Running: touch /tmp/nxf.wdl5ZbFxwU/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok 07:30:43 : INFO : Running: samtools sort -o 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam 07:30:49 : INFO : Execution Time = 0.10 minutes. CMD: samtools sort -o 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam 07:30:49 : INFO : Running: touch /tmp/nxf.wdl5ZbFxwU/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_gene_reads.ok 07:30:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 07:30:51 : INFO : Execution Time = 0.03 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 07:30:51 : INFO : Running: touch /tmp/nxf.wdl5ZbFxwU/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 07:30:51 : INFO : Running: samtools sort -o 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp 07:30:52 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp 07:30:52 : INFO : Running: touch /tmp/nxf.wdl5ZbFxwU/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 07:30:52 : INFO : Running: samtools index 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 07:30:52 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 07:30:52 : INFO : Running: touch /tmp/nxf.wdl5ZbFxwU/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 07:30:52 : INFO : Running: samtools index 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 07:30:52 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 07:30:52 : INFO : Running: touch /tmp/nxf.wdl5ZbFxwU/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 07:30:52 : INFO : Running: create_report 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1' 07:31:10 : INFO : Execution Time = 0.30 minutes. CMD: create_report 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1' 07:31:10 : INFO : Running: touch /tmp/nxf.wdl5ZbFxwU/1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/igv_create_html.ok 07:31:10 : INFO : done.