07:37:09 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[200000], rate=12000000.00/min
[210000], rate=12600000.00/min
[220000], rate=13200000.00/min
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[620000], rate=18600000.00/min
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[640000], rate=19200000.00/min
[650000], rate=19500000.00/min
[660000], rate=19800000.00/min
[670000], rate=20100000.00/min
[680000], rate=20400000.00/min
[690000], rate=20700000.00/min
[700000], rate=21000000.00/min
[710000], rate=21300000.00/min
[720000], rate=21600000.00/min
[730000], rate=21900000.00/min
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[760000], rate=22800000.00/min
[770000], rate=23100000.00/min
[780000], rate=23400000.00/min
[790000], rate=15800000.00/min
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[810000], rate=16200000.00/min
[820000], rate=16400000.00/min
[830000], rate=16600000.00/min
[840000], rate=16800000.00/min
[850000], rate=17000000.00/min
[860000], rate=17200000.00/min
[870000], rate=17400000.00/min
[880000], rate=17600000.00/min
[890000], rate=17800000.00/min
[900000], rate=18000000.00/min
[910000], rate=18200000.00/min
[920000], rate=18400000.00/min
[930000], rate=18600000.00/min
[940000], rate=18800000.00/min
[950000], rate=19000000.00/min
[960000], rate=19200000.00/min
[970000], rate=19400000.00/min
[980000], rate=19600000.00/min
[990000], rate=19800000.00/min
[1000000], rate=20000000.00/min
[1010000], rate=20200000.00/min
[1020000], rate=20400000.00/min
[1030000], rate=20600000.00/min
[1040000], rate=20800000.00/min
[1050000], rate=21000000.00/min
[1060000], rate=21200000.00/min
[1070000], rate=21400000.00/min
[1080000], rate=21600000.00/min
[1090000], rate=21800000.00/min
[1100000], rate=22000000.00/min
[1110000], rate=22200000.00/min
[1120000], rate=22400000.00/min
[1130000], rate=16950000.00/min
[1140000], rate=17100000.00/min
[1150000], rate=17250000.00/min
[1160000], rate=17400000.00/min
[1170000], rate=17550000.00/min
[1180000], rate=17700000.00/min
[1190000], rate=17850000.00/min
[1200000], rate=18000000.00/min
[1210000], rate=18150000.00/min
[1220000], rate=18300000.00/min
[1230000], rate=18450000.00/min
[1240000], rate=18600000.00/min
[1250000], rate=18750000.00/min
[1260000], rate=18900000.00/min
[1270000], rate=19050000.00/min
[1280000], rate=19200000.00/min
[1290000], rate=19350000.00/min
[1300000], rate=19500000.00/min
[1310000], rate=19650000.00/min
[1320000], rate=19800000.00/min
[1330000], rate=19950000.00/min
[1340000], rate=20100000.00/min
[1350000], rate=20250000.00/min
[1360000], rate=20400000.00/min
[1370000], rate=20550000.00/min
[1380000], rate=20700000.00/min
[1390000], rate=20850000.00/min
[1400000], rate=21000000.00/min
[1410000], rate=21150000.00/min
[1420000], rate=17040000.00/min
[1430000], rate=17160000.00/min
[1440000], rate=17280000.00/min
[1450000], rate=17400000.00/min
[1460000], rate=17520000.00/min
[1470000], rate=17640000.00/min
[1480000], rate=17760000.00/min
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[1500000], rate=18000000.00/min
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[1520000], rate=18240000.00/min
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[1540000], rate=18480000.00/min
[1550000], rate=18600000.00/min
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[1580000], rate=18960000.00/min
[1590000], rate=19080000.00/min
[1600000], rate=19200000.00/min
[1610000], rate=19320000.00/min
[1620000], rate=19440000.00/min
[1630000], rate=19560000.00/min
[1640000], rate=19680000.00/min
[1650000], rate=19800000.00/min
[1660000], rate=19920000.00/min
[1670000], rate=20040000.00/min
[1680000], rate=20160000.00/min
[1690000], rate=20280000.00/min
[1700000], rate=17000000.00/min
[1710000], rate=17100000.00/min
[1720000], rate=17200000.00/min
[1730000], rate=17300000.00/min
[1740000], rate=17400000.00/min
[1750000], rate=17500000.00/min
[1760000], rate=17600000.00/min
[1770000], rate=17700000.00/min
[1780000], rate=17800000.00/min
[1790000], rate=17900000.00/min
[1800000], rate=18000000.00/min
[1810000], rate=18100000.00/min
[1820000], rate=18200000.00/min
[1830000], rate=18300000.00/min
[1840000], rate=18400000.00/min
[1850000], rate=18500000.00/min
[1860000], rate=18600000.00/min
[1870000], rate=18700000.00/min
[1880000], rate=18800000.00/min
[1890000], rate=18900000.00/min
[1900000], rate=19000000.00/min
[1910000], rate=19100000.00/min
[1920000], rate=19200000.00/min
[1930000], rate=19300000.00/min
[1940000], rate=19400000.00/min
[1950000], rate=19500000.00/min
[1960000], rate=19600000.00/min
[1970000], rate=19700000.00/min
[1980000], rate=19800000.00/min
[1990000], rate=17057142.86/min
[2000000], rate=17142857.14/min
[2010000], rate=17228571.43/min
[2020000], rate=17314285.71/min
[2030000], rate=17400000.00/min
[2040000], rate=17485714.29/min
[2050000], rate=17571428.57/min
[2060000], rate=17657142.86/min
[2070000], rate=17742857.14/min
[2080000], rate=17828571.43/min
[2090000], rate=17914285.71/min
[2100000], rate=18000000.00/min
[2110000], rate=18085714.29/min
[2120000], rate=18171428.57/min
[2130000], rate=18257142.86/min
[2140000], rate=18342857.14/min
[2150000], rate=18428571.43/min
[2160000], rate=18514285.71/min 07:37:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_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.
-BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns: identified 360 cancer introns
07:37:21 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns.prelim
07:37:21 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/prelim_introns.ok
07:37:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns
07:37:22 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns
07:37:22 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/introns_filtered.ok
07:37:22 : INFO : -found 170 cancer introns
07:37:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns --cancer_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed
07:37:22 : INFO : Creating the BED File.
07:37:23 : INFO : Saving Bed File as BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed
07:37:23 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns --cancer_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed
07:37:23 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/intron_igv_bed.ok
07:37:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed --bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
07:37:35 : INFO : Execution Time = 0.20 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed --bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1
07:37:35 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/reads_alignments_extracted.ok
07:37:35 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.bam
07:37:35 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.bam
07:37:35 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/sort_cancer_intron_reads.ok
07:37:35 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.bam
07:37:49 : INFO : Execution Time = 0.23 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.bam
07:37:49 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/sort_gene_reads.ok
07:37:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.bam
07:37:53 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.bam
07:37:53 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:37:53 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp
07:37:54 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp
07:37:54 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:37:54 : INFO : Running: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam
07:37:55 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam
07:37:55 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:37:55 : INFO : Running: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.sorted.bam
07:37:55 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.sorted.bam
07:37:55 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:37:55 : INFO : Running: create_report BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1'
07:38:14 : INFO : Execution Time = 0.32 minutes. CMD: create_report BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1'
07:38:14 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/igv_create_html.ok
07:38:14 : INFO : done.