08:51:50 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10820000], rate=10470967.74/min
[10830000], rate=10480645.16/min
[10840000], rate=10490322.58/min
[10850000], rate=10500000.00/min
[10860000], rate=10509677.42/min
[10870000], rate=10519354.84/min
[10880000], rate=10529032.26/min
[10890000], rate=10538709.68/min
[10900000], rate=10548387.10/min
[10910000], rate=10558064.52/min
[10920000], rate=10567741.94/min
[10930000], rate=10577419.35/min
[10940000], rate=10587096.77/min
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[10960000], rate=10606451.61/min
[10970000], rate=10616129.03/min
[10980000], rate=10625806.45/min
[10990000], rate=10466666.67/min
[11000000], rate=10476190.48/min
[11010000], rate=10485714.29/min
[11020000], rate=10495238.10/min
[11030000], rate=10504761.90/min
[11040000], rate=10514285.71/min
[11050000], rate=10523809.52/min
[11060000], rate=10533333.33/min
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[11100000], rate=10571428.57/min
[11110000], rate=10580952.38/min
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[11160000], rate=10462500.00/min
[11170000], rate=10471875.00/min
[11180000], rate=10481250.00/min
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[11200000], rate=10500000.00/min
[11210000], rate=10509375.00/min
[11220000], rate=10518750.00/min
[11230000], rate=10528125.00/min
[11240000], rate=10537500.00/min
[11250000], rate=10546875.00/min
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[11280000], rate=10575000.00/min
[11290000], rate=10584375.00/min
[11300000], rate=10593750.00/min
[11310000], rate=10603125.00/min
[11320000], rate=10612500.00/min
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[11350000], rate=10640625.00/min
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[11440000], rate=10560000.00/min
[11450000], rate=10569230.77/min
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[11470000], rate=10587692.31/min
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[11500000], rate=10615384.62/min
[11510000], rate=10624615.38/min
[11520000], rate=10633846.15/min
[11530000], rate=10643076.92/min
[11540000], rate=10652307.69/min
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[11560000], rate=10509090.91/min
[11570000], rate=10518181.82/min 08:53:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_dts-T1-TRNA-1_B23MHV2LT4_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.
-659_dts-T1-TRNA-1_B23MHV2LT4_1.introns: identified 7878 cancer introns
08:53:11 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim
08:53:11 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok
08:53:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns
08:53:11 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns
08:53:11 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok
08:53:11 : INFO : -found 2724 cancer introns
08:53:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:53:12 : INFO : Creating the BED File.
08:53:21 : INFO : Saving Bed File as 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:53:22 : INFO : Execution Time = 0.18 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:53:22 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok
08:53:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_dts-T1-TRNA-1_B23MHV2LT4_1
[W::hts_idx_load3] The index file is older than the data file: 659_dts-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
09:21:02 : INFO : Execution Time = 27.67 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_dts-T1-TRNA-1_B23MHV2LT4_1
09:21:02 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok
09:21:02 : INFO : Running: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam
09:21:03 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam
09:21:03 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok
09:21:03 : INFO : Running: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam
[bam_sort_core] merging from 95 files and 1 in-memory blocks...
09:49:01 : INFO : Execution Time = 27.97 minutes. CMD: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam
09:49:01 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_gene_reads.ok
09:49:01 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam
09:56:07 : INFO : Execution Time = 7.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam
09:56:07 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok
09:56:07 : INFO : Running: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
09:57:04 : INFO : Execution Time = 0.95 minutes. CMD: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp
09:57:04 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:57:04 : INFO : Running: samtools index 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam
09:57:10 : INFO : Execution Time = 0.10 minutes. CMD: samtools index 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam
09:57:10 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok
09:57:10 : INFO : Running: samtools index 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam
09:57:10 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam
09:57:10 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok
09:57:10 : INFO : Running: create_report 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_dts-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_dts-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_dts-T1-TRNA-1_B23MHV2LT4_1'
10:03:38 : INFO : Execution Time = 6.46 minutes. CMD: create_report 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_dts-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_dts-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_dts-T1-TRNA-1_B23MHV2LT4_1'
10:03:38 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/igv_create_html.ok
10:03:38 : INFO : done.