09:13:14 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[9680000], rate=16133333.33/min 09:14:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-b6a2e8-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-b6a2e8-R1_A23YTGFLT4_1.introns: identified 6723 cancer introns
09:14:01 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer.introns.prelim
09:14:01 : INFO : Running: touch /tmp/nxf.wpTUey9WdN/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok
09:14:01 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer.introns
09:14:01 : 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-b6a2e8-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer.introns
09:14:01 : INFO : Running: touch /tmp/nxf.wpTUey9WdN/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok
09:14:01 : INFO : -found 2371 cancer introns
09:14:01 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.introns.for_IGV.bed
09:14:01 : INFO : Creating the BED File.
09:14:07 : INFO : Saving Bed File as aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.introns.for_IGV.bed
09:14:07 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.introns.for_IGV.bed
09:14:07 : INFO : Running: touch /tmp/nxf.wpTUey9WdN/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok
09:14:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
09:31:58 : INFO : Execution Time = 17.84 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1
09:31:58 : INFO : Running: touch /tmp/nxf.wpTUey9WdN/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok
09:31:58 : INFO : Running: samtools sort -o aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer_intron_reads.bam
09:31:58 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer_intron_reads.bam
09:31:58 : INFO : Running: touch /tmp/nxf.wpTUey9WdN/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok
09:31:58 : INFO : Running: samtools sort -o aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.bam
[bam_sort_core] merging from 93 files and 1 in-memory blocks...
09:51:43 : INFO : Execution Time = 19.75 minutes. CMD: samtools sort -o aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.bam
09:51:43 : INFO : Running: touch /tmp/nxf.wpTUey9WdN/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok
09:51:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.bam
09:58:52 : INFO : Execution Time = 7.15 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.bam
09:58:52 : INFO : Running: touch /tmp/nxf.wpTUey9WdN/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
09:58:52 : INFO : Running: samtools sort -o aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
09:59:45 : INFO : Execution Time = 0.87 minutes. CMD: samtools sort -o aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp
09:59:45 : INFO : Running: touch /tmp/nxf.wpTUey9WdN/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:59:45 : INFO : Running: samtools index aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam
09:59:51 : INFO : Execution Time = 0.10 minutes. CMD: samtools index aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam
09:59:51 : INFO : Running: touch /tmp/nxf.wpTUey9WdN/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
09:59:51 : INFO : Running: samtools index aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam
09:59:51 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam
09:59:51 : INFO : Running: touch /tmp/nxf.wpTUey9WdN/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
09:59:51 : INFO : Running: create_report aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1'
10:05:30 : INFO : Execution Time = 5.64 minutes. CMD: create_report aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1'
10:05:30 : INFO : Running: touch /tmp/nxf.wpTUey9WdN/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok
10:05:30 : INFO : done.