20:13:00 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=30000000.00/min [510000], rate=30600000.00/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=23400000.00/min [790000], rate=23700000.00/min [800000], rate=24000000.00/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 [890000], rate=17800000.00/min [900000], rate=18000000.00/min [910000], rate=18200000.00/min [920000], rate=18400000.00/min [930000], rate=18600000.00/min [940000], rate=18800000.00/min [950000], rate=19000000.00/min [960000], rate=19200000.00/min [970000], rate=19400000.00/min [980000], rate=19600000.00/min 20:13:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.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. -BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns: identified 24 cancer introns 20:13:08 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim 20:13:08 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/prelim_introns.ok 20:13:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns 20:13:09 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns 20:13:09 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/introns_filtered.ok 20:13:09 : INFO : -found 12 cancer introns 20:13:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --cancer_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed 20:13:09 : INFO : Creating the BED File. 20:13:10 : INFO : Saving Bed File as BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed 20:13:10 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --cancer_introns BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed 20:13:10 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/intron_igv_bed.ok 20:13:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed --bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2 [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai 20:13:28 : INFO : Execution Time = 0.30 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed --bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2 20:13:28 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok 20:13:28 : INFO : Running: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.bam 20:13:28 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.bam 20:13:28 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok 20:13:28 : INFO : Running: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.bam [bam_sort_core] merging from 1 files and 1 in-memory blocks... 20:13:50 : INFO : Execution Time = 0.36 minutes. CMD: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.bam 20:13:50 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/sort_gene_reads.ok 20:13:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam 20:13:54 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam 20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp.ok 20:13:54 : INFO : Running: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp 20:13:54 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp 20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok 20:13:54 : INFO : Running: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 20:13:54 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.indexed.ok 20:13:54 : INFO : Running: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 20:13:54 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 20:13:54 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam.indexed.ok 20:13:54 : INFO : Running: create_report BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.ctat-splicing.igv.html --track-config BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2' 20:13:56 : INFO : Execution Time = 0.03 minutes. CMD: create_report BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.ctat-splicing.igv.html --track-config BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2' 20:13:56 : INFO : Running: touch /tmp/nxf.kML1s1dFTd/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/igv_create_html.ok 20:13:56 : INFO : done.