07:35:18 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[10000], rate=600000.00/min
[20000], rate=1200000.00/min
[30000], rate=1800000.00/min
[40000], rate=2400000.00/min
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[100000], rate=6000000.00/min
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[340000], rate=10200000.00/min
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[400000], rate=8000000.00/min
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[420000], rate=8400000.00/min
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[590000], rate=8850000.00/min
[600000], rate=9000000.00/min
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[760000], rate=9120000.00/min
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[840000], rate=10080000.00/min
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[870000], rate=8700000.00/min
[880000], rate=8800000.00/min
[890000], rate=8900000.00/min
[900000], rate=9000000.00/min
[910000], rate=9100000.00/min
[920000], rate=9200000.00/min
[930000], rate=9300000.00/min
[940000], rate=9400000.00/min
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[960000], rate=9600000.00/min
[970000], rate=9700000.00/min
[980000], rate=9800000.00/min
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[1000000], rate=10000000.00/min
[1010000], rate=10100000.00/min
[1020000], rate=10200000.00/min
[1030000], rate=8828571.43/min
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[1050000], rate=9000000.00/min
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[1170000], rate=10028571.43/min
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[1190000], rate=10200000.00/min
[1200000], rate=9000000.00/min
[1210000], rate=9075000.00/min
[1220000], rate=9150000.00/min
[1230000], rate=9225000.00/min
[1240000], rate=9300000.00/min
[1250000], rate=9375000.00/min
[1260000], rate=9450000.00/min
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[1280000], rate=9600000.00/min
[1290000], rate=9675000.00/min
[1300000], rate=9750000.00/min
[1310000], rate=9825000.00/min
[1320000], rate=9900000.00/min
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[1340000], rate=10050000.00/min
[1350000], rate=10125000.00/min
[1360000], rate=10200000.00/min 07:35:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00677_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00677_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_00677_B23MVV7LT4_1.introns: identified 238 cancer introns
07:35:34 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00677_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00677_B23MVV7LT4_1.cancer.introns.prelim
07:35:34 : INFO : Running: touch /tmp/nxf.XHAwZZ6rQU/tih_rna_sample_00677_B23MVV7LT4_1.chckpts/prelim_introns.ok
07:35:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00677_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00677_B23MVV7LT4_1.cancer.introns
07:35:35 : 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_00677_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00677_B23MVV7LT4_1.cancer.introns
07:35:35 : INFO : Running: touch /tmp/nxf.XHAwZZ6rQU/tih_rna_sample_00677_B23MVV7LT4_1.chckpts/introns_filtered.ok
07:35:35 : INFO : -found 105 cancer introns
07:35:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00677_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00677_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00677_B23MVV7LT4_1.introns.for_IGV.bed
07:35:35 : INFO : Creating the BED File.
07:35:36 : INFO : Saving Bed File as tih_rna_sample_00677_B23MVV7LT4_1.introns.for_IGV.bed
07:35:36 : INFO : Execution Time = 0.03 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00677_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00677_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00677_B23MVV7LT4_1.introns.for_IGV.bed
07:35:36 : INFO : Running: touch /tmp/nxf.XHAwZZ6rQU/tih_rna_sample_00677_B23MVV7LT4_1.chckpts/intron_igv_bed.ok
07:35:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00677_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00677_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00677_B23MVV7LT4_1
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00677_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
07:36:41 : INFO : Execution Time = 1.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00677_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00677_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00677_B23MVV7LT4_1
07:36:41 : INFO : Running: touch /tmp/nxf.XHAwZZ6rQU/tih_rna_sample_00677_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok
07:36:41 : INFO : Running: samtools sort -o tih_rna_sample_00677_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00677_B23MVV7LT4_1.cancer_intron_reads.bam
07:36:41 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o tih_rna_sample_00677_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00677_B23MVV7LT4_1.cancer_intron_reads.bam
07:36:41 : INFO : Running: touch /tmp/nxf.XHAwZZ6rQU/tih_rna_sample_00677_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok
07:36:42 : INFO : Running: samtools sort -o tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.bam
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
07:37:49 : INFO : Execution Time = 1.13 minutes. CMD: samtools sort -o tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.bam
07:37:49 : INFO : Running: touch /tmp/nxf.XHAwZZ6rQU/tih_rna_sample_00677_B23MVV7LT4_1.chckpts/sort_gene_reads.ok
07:37:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.bam
07:38:03 : INFO : Execution Time = 0.23 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.bam
07:38:03 : INFO : Running: touch /tmp/nxf.XHAwZZ6rQU/tih_rna_sample_00677_B23MVV7LT4_1.chckpts/tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:38:03 : INFO : Running: samtools sort -o tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp
07:38:04 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp
07:38:04 : INFO : Running: touch /tmp/nxf.XHAwZZ6rQU/tih_rna_sample_00677_B23MVV7LT4_1.chckpts/tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:38:04 : INFO : Running: samtools index tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.sifted.bam
07:38:04 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.sifted.bam
07:38:04 : INFO : Running: touch /tmp/nxf.XHAwZZ6rQU/tih_rna_sample_00677_B23MVV7LT4_1.chckpts/tih_rna_sample_00677_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:38:04 : INFO : Running: samtools index tih_rna_sample_00677_B23MVV7LT4_1.cancer_intron_reads.sorted.bam
07:38:04 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00677_B23MVV7LT4_1.cancer_intron_reads.sorted.bam
07:38:04 : INFO : Running: touch /tmp/nxf.XHAwZZ6rQU/tih_rna_sample_00677_B23MVV7LT4_1.chckpts/tih_rna_sample_00677_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:38:04 : INFO : Running: create_report tih_rna_sample_00677_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00677_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00677_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00677_B23MVV7LT4_1'
07:38:16 : INFO : Execution Time = 0.20 minutes. CMD: create_report tih_rna_sample_00677_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00677_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00677_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00677_B23MVV7LT4_1'
07:38:16 : INFO : Running: touch /tmp/nxf.XHAwZZ6rQU/tih_rna_sample_00677_B23MVV7LT4_1.chckpts/igv_create_html.ok
07:38:16 : INFO : done.