19:54:27 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[5730000], rate=12278571.43/min
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[5760000], rate=12342857.14/min
[5770000], rate=12364285.71/min
[5780000], rate=12385714.29/min
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[5800000], rate=12428571.43/min
[5810000], rate=12450000.00/min
[5820000], rate=12471428.57/min
[5830000], rate=12492857.14/min
[5840000], rate=12514285.71/min
[5850000], rate=12535714.29/min
[5860000], rate=12557142.86/min
[5870000], rate=12578571.43/min
[5880000], rate=12600000.00/min
[5890000], rate=12621428.57/min
[5900000], rate=12642857.14/min
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[5970000], rate=12351724.14/min
[5980000], rate=12372413.79/min
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[6020000], rate=12455172.41/min
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[6040000], rate=12496551.72/min
[6050000], rate=12517241.38/min
[6060000], rate=12537931.03/min
[6070000], rate=12558620.69/min
[6080000], rate=12579310.34/min
[6090000], rate=12600000.00/min
[6100000], rate=12620689.66/min
[6110000], rate=12641379.31/min
[6120000], rate=12662068.97/min
[6130000], rate=12682758.62/min
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[6150000], rate=12300000.00/min
[6160000], rate=12320000.00/min 19:55:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-7fa0fb-R1_A23YTGFLT4_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.
-aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns: identified 3867 cancer introns
19:55:07 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer.introns.prelim
19:55:07 : INFO : Running: touch /tmp/nxf.ucW5kF3RXX/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok
19:55:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer.introns
19:55:08 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer.introns
19:55:08 : INFO : Running: touch /tmp/nxf.ucW5kF3RXX/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok
19:55:08 : INFO : -found 1318 cancer introns
19:55:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns.for_IGV.bed
19:55:08 : INFO : Creating the BED File.
19:55:13 : INFO : Saving Bed File as aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns.for_IGV.bed
19:55:13 : INFO : Execution Time = 0.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns.for_IGV.bed
19:55:13 : INFO : Running: touch /tmp/nxf.ucW5kF3RXX/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok
19:55:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
20:09:04 : INFO : Execution Time = 13.85 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1
20:09:04 : INFO : Running: touch /tmp/nxf.ucW5kF3RXX/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok
20:09:04 : INFO : Running: samtools sort -o aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer_intron_reads.bam
20:09:05 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer_intron_reads.bam
20:09:05 : INFO : Running: touch /tmp/nxf.ucW5kF3RXX/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok
20:09:05 : INFO : Running: samtools sort -o aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.bam
[bam_sort_core] merging from 50 files and 1 in-memory blocks...
20:22:08 : INFO : Execution Time = 13.06 minutes. CMD: samtools sort -o aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.bam
20:22:08 : INFO : Running: touch /tmp/nxf.ucW5kF3RXX/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok
20:22:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.bam
20:25:42 : INFO : Execution Time = 3.56 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.bam
20:25:42 : INFO : Running: touch /tmp/nxf.ucW5kF3RXX/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
20:25:42 : INFO : Running: samtools sort -o aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
20:26:24 : INFO : Execution Time = 0.71 minutes. CMD: samtools sort -o aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp
20:26:24 : INFO : Running: touch /tmp/nxf.ucW5kF3RXX/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
20:26:24 : INFO : Running: samtools index aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam
20:26:29 : INFO : Execution Time = 0.08 minutes. CMD: samtools index aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam
20:26:29 : INFO : Running: touch /tmp/nxf.ucW5kF3RXX/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
20:26:29 : INFO : Running: samtools index aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam
20:26:29 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam
20:26:29 : INFO : Running: touch /tmp/nxf.ucW5kF3RXX/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
20:26:29 : INFO : Running: create_report aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1'
20:31:49 : INFO : Execution Time = 5.33 minutes. CMD: create_report aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1'
20:31:49 : INFO : Running: touch /tmp/nxf.ucW5kF3RXX/aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok
20:31:49 : INFO : done.