07:29:57 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[150000], rate=9000000.00/min
[160000], rate=9600000.00/min
[170000], rate=10200000.00/min
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[250000], rate=15000000.00/min
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[300000], rate=18000000.00/min
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[440000], rate=13200000.00/min
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[460000], rate=13800000.00/min
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[490000], rate=14700000.00/min
[500000], rate=15000000.00/min
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[520000], rate=15600000.00/min
[530000], rate=15900000.00/min
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[560000], rate=11200000.00/min
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[590000], rate=11800000.00/min
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[650000], rate=13000000.00/min
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[680000], rate=13600000.00/min
[690000], rate=13800000.00/min
[700000], rate=14000000.00/min
[710000], rate=14200000.00/min
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[730000], rate=14600000.00/min
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[770000], rate=15400000.00/min
[780000], rate=15600000.00/min
[790000], rate=15800000.00/min
[800000], rate=12000000.00/min
[810000], rate=12150000.00/min
[820000], rate=12300000.00/min
[830000], rate=12450000.00/min
[840000], rate=12600000.00/min
[850000], rate=12750000.00/min
[860000], rate=12900000.00/min
[870000], rate=13050000.00/min
[880000], rate=13200000.00/min
[890000], rate=13350000.00/min
[900000], rate=13500000.00/min
[910000], rate=13650000.00/min
[920000], rate=13800000.00/min
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[940000], rate=14100000.00/min
[950000], rate=14250000.00/min
[960000], rate=14400000.00/min
[970000], rate=14550000.00/min
[980000], rate=14700000.00/min
[990000], rate=14850000.00/min
[1000000], rate=15000000.00/min
[1010000], rate=15150000.00/min
[1020000], rate=15300000.00/min
[1030000], rate=12360000.00/min
[1040000], rate=12480000.00/min
[1050000], rate=12600000.00/min
[1060000], rate=12720000.00/min
[1070000], rate=12840000.00/min
[1080000], rate=12960000.00/min
[1090000], rate=13080000.00/min
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[1120000], rate=13440000.00/min
[1130000], rate=13560000.00/min
[1140000], rate=13680000.00/min
[1150000], rate=13800000.00/min
[1160000], rate=13920000.00/min
[1170000], rate=14040000.00/min
[1180000], rate=14160000.00/min
[1190000], rate=14280000.00/min
[1200000], rate=14400000.00/min
[1210000], rate=14520000.00/min
[1220000], rate=14640000.00/min
[1230000], rate=14760000.00/min
[1240000], rate=14880000.00/min
[1250000], rate=15000000.00/min
[1260000], rate=12600000.00/min
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[1290000], rate=12900000.00/min
[1300000], rate=13000000.00/min
[1310000], rate=13100000.00/min
[1320000], rate=13200000.00/min
[1330000], rate=13300000.00/min
[1340000], rate=13400000.00/min
[1350000], rate=13500000.00/min
[1360000], rate=13600000.00/min
[1370000], rate=13700000.00/min
[1380000], rate=13800000.00/min
[1390000], rate=13900000.00/min
[1400000], rate=14000000.00/min
[1410000], rate=14100000.00/min
[1420000], rate=14200000.00/min
[1430000], rate=14300000.00/min
[1440000], rate=14400000.00/min
[1450000], rate=14500000.00/min
[1460000], rate=14600000.00/min
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[1480000], rate=14800000.00/min
[1490000], rate=14900000.00/min
[1500000], rate=15000000.00/min
[1510000], rate=12942857.14/min
[1520000], rate=13028571.43/min
[1530000], rate=13114285.71/min
[1540000], rate=13200000.00/min
[1550000], rate=13285714.29/min
[1560000], rate=13371428.57/min
[1570000], rate=13457142.86/min
[1580000], rate=13542857.14/min
[1590000], rate=13628571.43/min
[1600000], rate=13714285.71/min
[1610000], rate=13800000.00/min
[1620000], rate=13885714.29/min
[1630000], rate=13971428.57/min
[1640000], rate=14057142.86/min
[1650000], rate=14142857.14/min
[1660000], rate=14228571.43/min
[1670000], rate=14314285.71/min
[1680000], rate=14400000.00/min
[1690000], rate=14485714.29/min
[1700000], rate=14571428.57/min
[1710000], rate=14657142.86/min
[1720000], rate=14742857.14/min
[1730000], rate=14828571.43/min
[1740000], rate=14914285.71/min
[1750000], rate=15000000.00/min
[1760000], rate=15085714.29/min
[1770000], rate=13275000.00/min 07:30:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.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.
-22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns: identified 201 cancer introns
07:30:10 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim
07:30:10 : INFO : Running: touch /tmp/nxf.P2Uf6P1zUO/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/prelim_introns.ok
07:30:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim --min_total_reads 5 > 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns
07:30:11 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim --min_total_reads 5 > 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns
07:30:11 : INFO : Running: touch /tmp/nxf.P2Uf6P1zUO/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/introns_filtered.ok
07:30:11 : INFO : -found 79 cancer introns
07:30:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns --cancer_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
07:30:11 : INFO : Creating the BED File.
07:30:12 : INFO : Saving Bed File as 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
07:30:12 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns --cancer_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
07:30:12 : INFO : Running: touch /tmp/nxf.P2Uf6P1zUO/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/intron_igv_bed.ok
07:30:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed --bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --output_prefix 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
07:30:16 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed --bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --output_prefix 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3
07:30:16 : INFO : Running: touch /tmp/nxf.P2Uf6P1zUO/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/reads_alignments_extracted.ok
07:30:16 : INFO : Running: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.bam
07:30:16 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.bam
07:30:16 : INFO : Running: touch /tmp/nxf.P2Uf6P1zUO/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/sort_cancer_intron_reads.ok
07:30:16 : INFO : Running: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.bam
07:30:20 : INFO : Execution Time = 0.06 minutes. CMD: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.bam
07:30:20 : INFO : Running: touch /tmp/nxf.P2Uf6P1zUO/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/sort_gene_reads.ok
07:30:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp --keep_secondary 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam
07:30:21 : INFO : Execution Time = 0.03 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp --keep_secondary 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam
07:30:21 : INFO : Running: touch /tmp/nxf.P2Uf6P1zUO/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp.ok
07:30:21 : INFO : Running: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp
07:30:22 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp
07:30:22 : INFO : Running: touch /tmp/nxf.P2Uf6P1zUO/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:30:22 : INFO : Running: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam
07:30:23 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam
07:30:23 : INFO : Running: touch /tmp/nxf.P2Uf6P1zUO/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.indexed.ok
07:30:23 : INFO : Running: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam
07:30:23 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam
07:30:23 : INFO : Running: touch /tmp/nxf.P2Uf6P1zUO/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam.indexed.ok
07:30:23 : INFO : Running: create_report 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.ctat-splicing.igv.html --track-config 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3'
07:30:33 : INFO : Execution Time = 0.16 minutes. CMD: create_report 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.ctat-splicing.igv.html --track-config 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3'
07:30:33 : INFO : Running: touch /tmp/nxf.P2Uf6P1zUO/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/igv_create_html.ok
07:30:33 : INFO : done.