07:30:21 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[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
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[250000], rate=15000000.00/min
[260000], rate=15600000.00/min
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[280000], rate=16800000.00/min
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[300000], rate=18000000.00/min
[310000], rate=18600000.00/min
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[330000], rate=19800000.00/min
[340000], rate=20400000.00/min
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[400000], rate=24000000.00/min
[410000], rate=24600000.00/min
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[440000], rate=26400000.00/min
[450000], rate=27000000.00/min
[460000], rate=27600000.00/min
[470000], rate=28200000.00/min
[480000], rate=14400000.00/min
[490000], rate=14700000.00/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=23400000.00/min
[790000], rate=23700000.00/min
[800000], rate=24000000.00/min
[810000], rate=24300000.00/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
[990000], rate=19800000.00/min
[1000000], rate=20000000.00/min
[1010000], rate=20200000.00/min
[1020000], rate=20400000.00/min
[1030000], rate=20600000.00/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=17250000.00/min
[1160000], rate=17400000.00/min
[1170000], rate=17550000.00/min
[1180000], rate=17700000.00/min
[1190000], rate=17850000.00/min
[1200000], rate=18000000.00/min
[1210000], rate=18150000.00/min
[1220000], rate=18300000.00/min
[1230000], rate=18450000.00/min
[1240000], rate=18600000.00/min
[1250000], rate=18750000.00/min 07:30:30 : 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
07:30:30 : 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
07:30:30 : INFO : Running: touch /tmp/nxf.rfYdnthSXo/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok
07:30:30 : 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
07:30:31 : 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
07:30:31 : INFO : Running: touch /tmp/nxf.rfYdnthSXo/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok
07:30:31 : INFO : -found 31 cancer introns
07:30:31 : 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
07:30:31 : INFO : Creating the BED File.
07:30:31 : INFO : Saving Bed File as SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
07:30:31 : 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
07:30:31 : INFO : Running: touch /tmp/nxf.rfYdnthSXo/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
07:30:31 : 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
07:30:32 : INFO : Execution Time = 0.01 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
07:30:32 : INFO : Running: touch /tmp/nxf.rfYdnthSXo/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
07:30:32 : 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
07:30:32 : 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
07:30:32 : INFO : Running: touch /tmp/nxf.rfYdnthSXo/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
07:30:32 : 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
07:30:33 : 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
07:30:33 : INFO : Running: touch /tmp/nxf.rfYdnthSXo/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
07:30:33 : 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
07:30:33 : 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
07:30:33 : INFO : Running: touch /tmp/nxf.rfYdnthSXo/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:30:33 : 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
07:30:34 : 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
07:30:34 : INFO : Running: touch /tmp/nxf.rfYdnthSXo/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:30:34 : INFO : Running: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
07:30:34 : INFO : Execution Time = 0.00 minutes. CMD: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
07:30:34 : INFO : Running: touch /tmp/nxf.rfYdnthSXo/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:30:34 : INFO : Running: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
07:30:34 : INFO : Execution Time = 0.00 minutes. CMD: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
07:30:34 : INFO : Running: touch /tmp/nxf.rfYdnthSXo/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:30:34 : 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'
07:30:38 : INFO : Execution Time = 0.07 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'
07:30:38 : INFO : Running: touch /tmp/nxf.rfYdnthSXo/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok
07:30:38 : INFO : done.