08:31:38 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[5640000], rate=18800000.00/min
[5650000], rate=18833333.33/min
[5660000], rate=18866666.67/min
[5670000], rate=18900000.00/min
[5680000], rate=18933333.33/min
[5690000], rate=18966666.67/min
[5700000], rate=19000000.00/min
[5710000], rate=19033333.33/min
[5720000], rate=19066666.67/min
[5730000], rate=19100000.00/min
[5740000], rate=19133333.33/min
[5750000], rate=19166666.67/min
[5760000], rate=19200000.00/min
[5770000], rate=19233333.33/min
[5780000], rate=19266666.67/min
[5790000], rate=19300000.00/min
[5800000], rate=19333333.33/min
[5810000], rate=19366666.67/min
[5820000], rate=19400000.00/min
[5830000], rate=19433333.33/min
[5840000], rate=18442105.26/min
[5850000], rate=18473684.21/min
[5860000], rate=18505263.16/min
[5870000], rate=18536842.11/min
[5880000], rate=18568421.05/min
[5890000], rate=18600000.00/min
[5900000], rate=18631578.95/min
[5910000], rate=18663157.89/min
[5920000], rate=18694736.84/min
[5930000], rate=18726315.79/min
[5940000], rate=18757894.74/min
[5950000], rate=18789473.68/min
[5960000], rate=18821052.63/min
[5970000], rate=18852631.58/min
[5980000], rate=18884210.53/min
[5990000], rate=18915789.47/min
[6000000], rate=18947368.42/min
[6010000], rate=18978947.37/min
[6020000], rate=19010526.32/min
[6030000], rate=19042105.26/min
[6040000], rate=19073684.21/min
[6050000], rate=19105263.16/min
[6060000], rate=19136842.11/min
[6070000], rate=19168421.05/min
[6080000], rate=19200000.00/min
[6090000], rate=19231578.95/min
[6100000], rate=19263157.89/min
[6110000], rate=19294736.84/min
[6120000], rate=19326315.79/min
[6130000], rate=19357894.74/min
[6140000], rate=19389473.68/min
[6150000], rate=19421052.63/min
[6160000], rate=19452631.58/min
[6170000], rate=19484210.53/min
[6180000], rate=19515789.47/min
[6190000], rate=19547368.42/min
[6200000], rate=18600000.00/min
[6210000], rate=18630000.00/min
[6220000], rate=18660000.00/min
[6230000], rate=18690000.00/min
[6240000], rate=18720000.00/min
[6250000], rate=18750000.00/min
[6260000], rate=18780000.00/min
[6270000], rate=18810000.00/min
[6280000], rate=18840000.00/min
[6290000], rate=18870000.00/min
[6300000], rate=18900000.00/min
[6310000], rate=18930000.00/min
[6320000], rate=18960000.00/min
[6330000], rate=18990000.00/min
[6340000], rate=19020000.00/min
[6350000], rate=19050000.00/min
[6360000], rate=19080000.00/min
[6370000], rate=19110000.00/min
[6380000], rate=19140000.00/min 08:32:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00124_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00124_B23WHTKLT4_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.
-tih_rna_sample_00124_B23WHTKLT4_2.introns: identified 5859 cancer introns
08:32:06 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00124_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00124_B23WHTKLT4_2.cancer.introns.prelim
08:32:06 : INFO : Running: touch /tmp/nxf.R2AIcoMOQd/tih_rna_sample_00124_B23WHTKLT4_2.chckpts/prelim_introns.ok
08:32:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00124_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00124_B23WHTKLT4_2.cancer.introns
08:32:06 : 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_00124_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00124_B23WHTKLT4_2.cancer.introns
08:32:06 : INFO : Running: touch /tmp/nxf.R2AIcoMOQd/tih_rna_sample_00124_B23WHTKLT4_2.chckpts/introns_filtered.ok
08:32:06 : INFO : -found 2277 cancer introns
08:32:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00124_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00124_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00124_B23WHTKLT4_2.introns.for_IGV.bed
08:32:06 : INFO : Creating the BED File.
08:32:10 : INFO : Saving Bed File as tih_rna_sample_00124_B23WHTKLT4_2.introns.for_IGV.bed
08:32:11 : INFO : Execution Time = 0.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00124_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00124_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00124_B23WHTKLT4_2.introns.for_IGV.bed
08:32:11 : INFO : Running: touch /tmp/nxf.R2AIcoMOQd/tih_rna_sample_00124_B23WHTKLT4_2.chckpts/intron_igv_bed.ok
08:32:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00124_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00124_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00124_B23WHTKLT4_2
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00124_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam.bai
08:45:07 : INFO : Execution Time = 12.93 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00124_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00124_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00124_B23WHTKLT4_2
08:45:07 : INFO : Running: touch /tmp/nxf.R2AIcoMOQd/tih_rna_sample_00124_B23WHTKLT4_2.chckpts/reads_alignments_extracted.ok
08:45:07 : INFO : Running: samtools sort -o tih_rna_sample_00124_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00124_B23WHTKLT4_2.cancer_intron_reads.bam
08:45:07 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00124_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00124_B23WHTKLT4_2.cancer_intron_reads.bam
08:45:07 : INFO : Running: touch /tmp/nxf.R2AIcoMOQd/tih_rna_sample_00124_B23WHTKLT4_2.chckpts/sort_cancer_intron_reads.ok
08:45:07 : INFO : Running: samtools sort -o tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.bam tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.bam
[bam_sort_core] merging from 73 files and 1 in-memory blocks...
09:00:15 : INFO : Execution Time = 15.14 minutes. CMD: samtools sort -o tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.bam tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.bam
09:00:15 : INFO : Running: touch /tmp/nxf.R2AIcoMOQd/tih_rna_sample_00124_B23WHTKLT4_2.chckpts/sort_gene_reads.ok
09:00:15 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.bam
09:05:04 : INFO : Execution Time = 4.81 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.bam
09:05:04 : INFO : Running: touch /tmp/nxf.R2AIcoMOQd/tih_rna_sample_00124_B23WHTKLT4_2.chckpts/tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
09:05:04 : INFO : Running: samtools sort -o tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.sifted.bam tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
09:05:47 : INFO : Execution Time = 0.71 minutes. CMD: samtools sort -o tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.sifted.bam tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp
09:05:47 : INFO : Running: touch /tmp/nxf.R2AIcoMOQd/tih_rna_sample_00124_B23WHTKLT4_2.chckpts/tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:05:47 : INFO : Running: samtools index tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.sifted.bam
09:05:51 : INFO : Execution Time = 0.08 minutes. CMD: samtools index tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.sifted.bam
09:05:51 : INFO : Running: touch /tmp/nxf.R2AIcoMOQd/tih_rna_sample_00124_B23WHTKLT4_2.chckpts/tih_rna_sample_00124_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
09:05:51 : INFO : Running: samtools index tih_rna_sample_00124_B23WHTKLT4_2.cancer_intron_reads.sorted.bam
09:05:51 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00124_B23WHTKLT4_2.cancer_intron_reads.sorted.bam
09:05:51 : INFO : Running: touch /tmp/nxf.R2AIcoMOQd/tih_rna_sample_00124_B23WHTKLT4_2.chckpts/tih_rna_sample_00124_B23WHTKLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
09:05:51 : INFO : Running: create_report tih_rna_sample_00124_B23WHTKLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00124_B23WHTKLT4_2.ctat-splicing.igv.html --track-config tih_rna_sample_00124_B23WHTKLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00124_B23WHTKLT4_2'
09:10:58 : INFO : Execution Time = 5.11 minutes. CMD: create_report tih_rna_sample_00124_B23WHTKLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00124_B23WHTKLT4_2.ctat-splicing.igv.html --track-config tih_rna_sample_00124_B23WHTKLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00124_B23WHTKLT4_2'
09:10:58 : INFO : Running: touch /tmp/nxf.R2AIcoMOQd/tih_rna_sample_00124_B23WHTKLT4_2.chckpts/igv_create_html.ok
09:10:58 : INFO : done.