07:32:51 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=16200000.00/min [280000], rate=8400000.00/min [290000], rate=8700000.00/min [300000], rate=9000000.00/min [310000], rate=9300000.00/min [320000], rate=9600000.00/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], rate=11700000.00/min [400000], rate=12000000.00/min [410000], rate=12300000.00/min [420000], rate=12600000.00/min [430000], rate=12900000.00/min [440000], rate=13200000.00/min [450000], rate=13500000.00/min [460000], rate=13800000.00/min [470000], rate=9400000.00/min [480000], rate=9600000.00/min [490000], rate=9800000.00/min [500000], rate=10000000.00/min [510000], rate=10200000.00/min [520000], rate=10400000.00/min [530000], rate=10600000.00/min [540000], rate=10800000.00/min [550000], rate=11000000.00/min 07:33:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_CRX_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_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 830 cancer introns 07:33:00 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim 07:33:00 : INFO : Running: touch /tmp/nxf.hnkK1uHUB6/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok 07:33:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 07:33:00 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 07:33:00 : INFO : Running: touch /tmp/nxf.hnkK1uHUB6/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok 07:33:00 : INFO : -found 21 cancer introns 07:33:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 07:33:01 : INFO : Creating the BED File. 07:33:01 : INFO : Saving Bed File as 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 07:33:01 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 07:33:01 : INFO : Running: touch /tmp/nxf.hnkK1uHUB6/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok 07:33:01 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1 [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai 07:33:07 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1 07:33:07 : INFO : Running: touch /tmp/nxf.hnkK1uHUB6/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok 07:33:07 : INFO : Running: samtools sort -o 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 07:33:07 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 07:33:07 : INFO : Running: touch /tmp/nxf.hnkK1uHUB6/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok 07:33:07 : INFO : Running: samtools sort -o 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam 07:33:13 : INFO : Execution Time = 0.09 minutes. CMD: samtools sort -o 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam 07:33:13 : INFO : Running: touch /tmp/nxf.hnkK1uHUB6/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_gene_reads.ok 07:33:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 07:33:14 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 07:33:14 : INFO : Running: touch /tmp/nxf.hnkK1uHUB6/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 07:33:14 : INFO : Running: samtools sort -o 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp 07:33:14 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp 07:33:14 : INFO : Running: touch /tmp/nxf.hnkK1uHUB6/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 07:33:14 : INFO : Running: samtools index 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 07:33:15 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 07:33:15 : INFO : Running: touch /tmp/nxf.hnkK1uHUB6/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 07:33:15 : INFO : Running: samtools index 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 07:33:15 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 07:33:15 : INFO : Running: touch /tmp/nxf.hnkK1uHUB6/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 07:33:15 : INFO : Running: create_report 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1' 07:33:18 : INFO : Execution Time = 0.06 minutes. CMD: create_report 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1' 07:33:18 : INFO : Running: touch /tmp/nxf.hnkK1uHUB6/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/igv_create_html.ok 07:33:18 : INFO : done.