20:12:17 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=30000000.00/min [510000], rate=30600000.00/min [520000], rate=31200000.00/min [530000], rate=31800000.00/min [540000], rate=32400000.00/min [550000], rate=33000000.00/min [560000], rate=33600000.00/min [570000], rate=34200000.00/min [580000], rate=34800000.00/min [590000], rate=35400000.00/min [600000], rate=36000000.00/min [610000], rate=36600000.00/min [620000], rate=37200000.00/min [630000], rate=37800000.00/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=23400000.00/min [790000], rate=23700000.00/min [800000], rate=24000000.00/min [810000], rate=24300000.00/min [820000], rate=24600000.00/min [830000], rate=24900000.00/min [840000], rate=25200000.00/min [850000], rate=25500000.00/min [860000], rate=25800000.00/min [870000], rate=26100000.00/min [880000], rate=26400000.00/min [890000], rate=26700000.00/min [900000], rate=27000000.00/min [910000], rate=27300000.00/min [920000], rate=27600000.00/min [930000], rate=27900000.00/min [940000], rate=28200000.00/min [950000], rate=28500000.00/min [960000], rate=28800000.00/min [970000], rate=29100000.00/min [980000], rate=29400000.00/min [990000], rate=29700000.00/min [1000000], rate=30000000.00/min [1010000], rate=30300000.00/min [1020000], rate=30600000.00/min [1030000], rate=30900000.00/min [1040000], rate=20800000.00/min [1050000], rate=21000000.00/min [1060000], rate=21200000.00/min [1070000], rate=21400000.00/min [1080000], rate=21600000.00/min [1090000], rate=21800000.00/min [1100000], rate=22000000.00/min [1110000], rate=22200000.00/min [1120000], rate=22400000.00/min [1130000], rate=22600000.00/min [1140000], rate=22800000.00/min [1150000], rate=23000000.00/min [1160000], rate=23200000.00/min [1170000], rate=23400000.00/min [1180000], rate=23600000.00/min [1190000], rate=23800000.00/min [1200000], rate=24000000.00/min [1210000], rate=24200000.00/min [1220000], rate=24400000.00/min [1230000], rate=24600000.00/min [1240000], rate=24800000.00/min [1250000], rate=25000000.00/min 20:12:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > SkinN_FFPE_L01_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. -SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns: identified 71 cancer introns 20:12:25 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim 20:12:25 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok 20:12:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns 20:12:26 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns 20:12:26 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok 20:12:26 : INFO : -found 31 cancer introns 20:12:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns --cancer_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:12:26 : INFO : Creating the BED File. 20:12:27 : INFO : Saving Bed File as SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:12:27 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns --cancer_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:12:27 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok 20:12:27 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1 [W::hts_idx_load3] The index file is older than the data file: SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai 20:12:28 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1 20:12:28 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok 20:12:28 : INFO : Running: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam 20:12:28 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam 20:12:28 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok 20:12:28 : INFO : Running: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.bam 20:12:28 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.bam 20:12:28 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok 20:12:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 20:12:29 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 20:12:29 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 20:12:29 : INFO : Running: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp 20:12:29 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp 20:12:29 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 20:12:29 : INFO : Running: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 20:12:29 : INFO : Execution Time = 0.00 minutes. CMD: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 20:12:29 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 20:12:29 : INFO : Running: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 20:12:29 : INFO : Execution Time = 0.00 minutes. CMD: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 20:12:29 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 20:12:29 : INFO : Running: create_report SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1' 20:12:34 : INFO : Execution Time = 0.08 minutes. CMD: create_report SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1' 20:12:34 : INFO : Running: touch /tmp/nxf.UUcMBniUsZ/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok 20:12:34 : INFO : done.