07:36:44 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[30000], rate=1800000.00/min
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[710000], rate=21300000.00/min
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[780000], rate=15600000.00/min
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[840000], rate=16800000.00/min
[850000], rate=17000000.00/min
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[880000], rate=17600000.00/min
[890000], rate=17800000.00/min
[900000], rate=18000000.00/min
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[940000], rate=18800000.00/min
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[980000], rate=19600000.00/min
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[1000000], rate=20000000.00/min
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[1030000], rate=15450000.00/min
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[1400000], rate=16800000.00/min
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[1480000], rate=17760000.00/min
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[1500000], rate=18000000.00/min
[1510000], rate=18120000.00/min
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[1540000], rate=18480000.00/min
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[1560000], rate=18720000.00/min
[1570000], rate=18840000.00/min
[1580000], rate=18960000.00/min
[1590000], rate=19080000.00/min
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[1610000], rate=19320000.00/min
[1620000], rate=19440000.00/min
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[1660000], rate=16600000.00/min
[1670000], rate=16700000.00/min
[1680000], rate=16800000.00/min
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[1700000], rate=17000000.00/min
[1710000], rate=17100000.00/min
[1720000], rate=17200000.00/min
[1730000], rate=17300000.00/min
[1740000], rate=17400000.00/min
[1750000], rate=17500000.00/min
[1760000], rate=17600000.00/min
[1770000], rate=17700000.00/min
[1780000], rate=17800000.00/min
[1790000], rate=17900000.00/min
[1800000], rate=18000000.00/min
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[1830000], rate=18300000.00/min
[1840000], rate=18400000.00/min 07:36:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_SFA_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_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 475 cancer introns
07:36:55 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim
07:36:55 : INFO : Running: touch /tmp/nxf.s7aBc9lU6W/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok
07:36:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns
07:36:56 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns
07:36:56 : INFO : Running: touch /tmp/nxf.s7aBc9lU6W/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok
07:36:56 : INFO : -found 354 cancer introns
07:36:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
07:36:56 : INFO : Creating the BED File.
07:36:57 : INFO : Saving Bed File as 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
07:36:57 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
07:36:57 : INFO : Running: touch /tmp/nxf.s7aBc9lU6W/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok
07:36:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1
[W::hts_idx_load3] The index file is older than the data file: 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
07:37:50 : INFO : Execution Time = 0.89 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1
07:37:50 : INFO : Running: touch /tmp/nxf.s7aBc9lU6W/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok
07:37:50 : INFO : Running: samtools sort -o 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
07:37:51 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
07:37:51 : INFO : Running: touch /tmp/nxf.s7aBc9lU6W/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok
07:37:51 : INFO : Running: samtools sort -o 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
[bam_sort_core] merging from 4 files and 1 in-memory blocks...
07:38:58 : INFO : Execution Time = 1.12 minutes. CMD: samtools sort -o 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
07:38:58 : INFO : Running: touch /tmp/nxf.s7aBc9lU6W/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_gene_reads.ok
07:38:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam
07:39:14 : INFO : Execution Time = 0.28 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam
07:39:14 : INFO : Running: touch /tmp/nxf.s7aBc9lU6W/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:39:15 : INFO : Running: samtools sort -o 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
07:39:18 : INFO : Execution Time = 0.06 minutes. CMD: samtools sort -o 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
07:39:18 : INFO : Running: touch /tmp/nxf.s7aBc9lU6W/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:39:18 : INFO : Running: samtools index 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam
07:39:18 : INFO : Execution Time = 0.01 minutes. CMD: samtools index 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam
07:39:18 : INFO : Running: touch /tmp/nxf.s7aBc9lU6W/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:39:18 : INFO : Running: samtools index 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam
07:39:19 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam
07:39:19 : INFO : Running: touch /tmp/nxf.s7aBc9lU6W/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:39:19 : INFO : Running: create_report 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1'
07:39:53 : INFO : Execution Time = 0.58 minutes. CMD: create_report 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1'
07:39:53 : INFO : Running: touch /tmp/nxf.s7aBc9lU6W/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/igv_create_html.ok
07:39:53 : INFO : done.