09:10:02 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10900000], rate=17210526.32/min
[10910000], rate=17226315.79/min
[10920000], rate=17242105.26/min
[10930000], rate=17257894.74/min
[10940000], rate=17273684.21/min
[10950000], rate=17289473.68/min
[10960000], rate=17305263.16/min
[10970000], rate=17321052.63/min
[10980000], rate=17336842.11/min
[10990000], rate=17352631.58/min
[11000000], rate=17368421.05/min
[11010000], rate=17384210.53/min
[11020000], rate=17400000.00/min
[11030000], rate=17415789.47/min
[11040000], rate=17431578.95/min
[11050000], rate=17447368.42/min
[11060000], rate=17463157.89/min
[11070000], rate=17478947.37/min
[11080000], rate=17494736.84/min
[11090000], rate=17510526.32/min
[11100000], rate=17076923.08/min
[11110000], rate=17092307.69/min
[11120000], rate=17107692.31/min
[11130000], rate=17123076.92/min
[11140000], rate=17138461.54/min
[11150000], rate=17153846.15/min
[11160000], rate=17169230.77/min
[11170000], rate=17184615.38/min
[11180000], rate=17200000.00/min
[11190000], rate=17215384.62/min
[11200000], rate=17230769.23/min
[11210000], rate=17246153.85/min
[11220000], rate=17261538.46/min
[11230000], rate=17276923.08/min
[11240000], rate=17292307.69/min
[11250000], rate=17307692.31/min
[11260000], rate=17323076.92/min
[11270000], rate=17338461.54/min
[11280000], rate=17353846.15/min
[11290000], rate=17369230.77/min
[11300000], rate=17384615.38/min
[11310000], rate=17400000.00/min 09:10:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00599_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00599_B23MVV7LT4_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.
-tih_rna_sample_00599_B23MVV7LT4_1.introns: identified 5634 cancer introns
09:10:51 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00599_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00599_B23MVV7LT4_1.cancer.introns.prelim
09:10:51 : INFO : Running: touch /tmp/nxf.3tiB3VpOPA/tih_rna_sample_00599_B23MVV7LT4_1.chckpts/prelim_introns.ok
09:10:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00599_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00599_B23MVV7LT4_1.cancer.introns
09:10:51 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00599_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00599_B23MVV7LT4_1.cancer.introns
09:10:51 : INFO : Running: touch /tmp/nxf.3tiB3VpOPA/tih_rna_sample_00599_B23MVV7LT4_1.chckpts/introns_filtered.ok
09:10:51 : INFO : -found 2667 cancer introns
09:10:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00599_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00599_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00599_B23MVV7LT4_1.introns.for_IGV.bed
09:10:51 : INFO : Creating the BED File.
09:10:57 : INFO : Saving Bed File as tih_rna_sample_00599_B23MVV7LT4_1.introns.for_IGV.bed
09:10:58 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00599_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00599_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00599_B23MVV7LT4_1.introns.for_IGV.bed
09:10:58 : INFO : Running: touch /tmp/nxf.3tiB3VpOPA/tih_rna_sample_00599_B23MVV7LT4_1.chckpts/intron_igv_bed.ok
09:10:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00599_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00599_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00599_B23MVV7LT4_1
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
09:32:01 : INFO : Execution Time = 21.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00599_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00599_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00599_B23MVV7LT4_1
09:32:01 : INFO : Running: touch /tmp/nxf.3tiB3VpOPA/tih_rna_sample_00599_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok
09:32:01 : INFO : Running: samtools sort -o tih_rna_sample_00599_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00599_B23MVV7LT4_1.cancer_intron_reads.bam
09:32:01 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00599_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00599_B23MVV7LT4_1.cancer_intron_reads.bam
09:32:01 : INFO : Running: touch /tmp/nxf.3tiB3VpOPA/tih_rna_sample_00599_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok
09:32:01 : INFO : Running: samtools sort -o tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.bam
[bam_sort_core] merging from 99 files and 1 in-memory blocks...
09:55:09 : INFO : Execution Time = 23.12 minutes. CMD: samtools sort -o tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.bam
09:55:09 : INFO : Running: touch /tmp/nxf.3tiB3VpOPA/tih_rna_sample_00599_B23MVV7LT4_1.chckpts/sort_gene_reads.ok
09:55:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.bam
10:02:17 : INFO : Execution Time = 7.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.bam
10:02:17 : INFO : Running: touch /tmp/nxf.3tiB3VpOPA/tih_rna_sample_00599_B23MVV7LT4_1.chckpts/tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok
10:02:17 : INFO : Running: samtools sort -o tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
10:03:04 : INFO : Execution Time = 0.79 minutes. CMD: samtools sort -o tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp
10:03:04 : INFO : Running: touch /tmp/nxf.3tiB3VpOPA/tih_rna_sample_00599_B23MVV7LT4_1.chckpts/tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:03:04 : INFO : Running: samtools index tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.sifted.bam
10:03:10 : INFO : Execution Time = 0.09 minutes. CMD: samtools index tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.sifted.bam
10:03:10 : INFO : Running: touch /tmp/nxf.3tiB3VpOPA/tih_rna_sample_00599_B23MVV7LT4_1.chckpts/tih_rna_sample_00599_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok
10:03:10 : INFO : Running: samtools index tih_rna_sample_00599_B23MVV7LT4_1.cancer_intron_reads.sorted.bam
10:03:10 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00599_B23MVV7LT4_1.cancer_intron_reads.sorted.bam
10:03:10 : INFO : Running: touch /tmp/nxf.3tiB3VpOPA/tih_rna_sample_00599_B23MVV7LT4_1.chckpts/tih_rna_sample_00599_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok
10:03:10 : INFO : Running: create_report tih_rna_sample_00599_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00599_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00599_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00599_B23MVV7LT4_1'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
10:09:08 : INFO : Execution Time = 5.97 minutes. CMD: create_report tih_rna_sample_00599_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00599_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00599_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00599_B23MVV7LT4_1'
10:09:08 : INFO : Running: touch /tmp/nxf.3tiB3VpOPA/tih_rna_sample_00599_B23MVV7LT4_1.chckpts/igv_create_html.ok
10:09:08 : INFO : done.