07:38:37 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[80000], rate=4800000.00/min
[90000], rate=5400000.00/min
[100000], rate=6000000.00/min
[110000], rate=6600000.00/min
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[200000], rate=12000000.00/min
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[360000], rate=10800000.00/min
[370000], rate=11100000.00/min
[380000], rate=11400000.00/min
[390000], rate=11700000.00/min
[400000], rate=12000000.00/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
[510000], rate=15300000.00/min
[520000], rate=15600000.00/min
[530000], rate=15900000.00/min
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[550000], rate=16500000.00/min
[560000], rate=16800000.00/min
[570000], rate=17100000.00/min
[580000], rate=17400000.00/min
[590000], rate=17700000.00/min
[600000], rate=18000000.00/min
[610000], rate=18300000.00/min
[620000], rate=12400000.00/min
[630000], rate=12600000.00/min
[640000], rate=12800000.00/min
[650000], rate=13000000.00/min
[660000], rate=13200000.00/min
[670000], rate=13400000.00/min
[680000], rate=13600000.00/min
[690000], rate=13800000.00/min
[700000], rate=14000000.00/min
[710000], rate=14200000.00/min
[720000], rate=14400000.00/min
[730000], rate=14600000.00/min
[740000], rate=14800000.00/min
[750000], rate=15000000.00/min
[760000], rate=15200000.00/min
[770000], rate=15400000.00/min
[780000], rate=15600000.00/min
[790000], rate=15800000.00/min
[800000], rate=16000000.00/min
[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=15000000.00/min
[1010000], rate=15150000.00/min
[1020000], rate=15300000.00/min
[1030000], rate=15450000.00/min
[1040000], rate=15600000.00/min
[1050000], rate=15750000.00/min
[1060000], rate=15900000.00/min
[1070000], rate=16050000.00/min
[1080000], rate=16200000.00/min
[1090000], rate=16350000.00/min
[1100000], rate=16500000.00/min
[1110000], rate=16650000.00/min
[1120000], rate=16800000.00/min
[1130000], rate=16950000.00/min
[1140000], rate=17100000.00/min
[1150000], rate=17250000.00/min
[1160000], rate=17400000.00/min
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[1180000], rate=17700000.00/min
[1190000], rate=17850000.00/min
[1200000], rate=18000000.00/min
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[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=15360000.00/min
[1290000], rate=15480000.00/min
[1300000], rate=15600000.00/min
[1310000], rate=15720000.00/min
[1320000], rate=15840000.00/min
[1330000], rate=15960000.00/min
[1340000], rate=16080000.00/min
[1350000], rate=16200000.00/min
[1360000], rate=16320000.00/min
[1370000], rate=16440000.00/min
[1380000], rate=16560000.00/min
[1390000], rate=16680000.00/min
[1400000], rate=16800000.00/min
[1410000], rate=16920000.00/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
[1490000], rate=17880000.00/min
[1500000], rate=18000000.00/min
[1510000], rate=18120000.00/min
[1520000], rate=18240000.00/min
[1530000], rate=18360000.00/min
[1540000], rate=18480000.00/min
[1550000], rate=18600000.00/min
[1560000], rate=18720000.00/min
[1570000], rate=15700000.00/min
[1580000], rate=15800000.00/min
[1590000], rate=15900000.00/min
[1600000], rate=16000000.00/min
[1610000], rate=16100000.00/min
[1620000], rate=16200000.00/min
[1630000], rate=16300000.00/min
[1640000], rate=16400000.00/min
[1650000], rate=16500000.00/min
[1660000], rate=16600000.00/min
[1670000], rate=16700000.00/min
[1680000], rate=16800000.00/min
[1690000], rate=16900000.00/min 07:38:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00461_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00461_B23WHTKLT4_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_00461_B23WHTKLT4_1.introns: identified 769 cancer introns
07:38:49 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00461_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00461_B23WHTKLT4_1.cancer.introns.prelim
07:38:49 : INFO : Running: touch /tmp/nxf.Z1txKUq3z2/tih_rna_sample_00461_B23WHTKLT4_1.chckpts/prelim_introns.ok
07:38:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00461_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00461_B23WHTKLT4_1.cancer.introns
07:38:49 : 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_00461_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00461_B23WHTKLT4_1.cancer.introns
07:38:49 : INFO : Running: touch /tmp/nxf.Z1txKUq3z2/tih_rna_sample_00461_B23WHTKLT4_1.chckpts/introns_filtered.ok
07:38:49 : INFO : -found 622 cancer introns
07:38:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00461_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00461_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00461_B23WHTKLT4_1.introns.for_IGV.bed
07:38:50 : INFO : Creating the BED File.
07:38:52 : INFO : Saving Bed File as tih_rna_sample_00461_B23WHTKLT4_1.introns.for_IGV.bed
07:38:52 : INFO : Execution Time = 0.04 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00461_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00461_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00461_B23WHTKLT4_1.introns.for_IGV.bed
07:38:52 : INFO : Running: touch /tmp/nxf.Z1txKUq3z2/tih_rna_sample_00461_B23WHTKLT4_1.chckpts/intron_igv_bed.ok
07:38:52 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00461_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00461_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00461_B23WHTKLT4_1
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00461_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
07:39:55 : INFO : Execution Time = 1.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00461_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00461_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00461_B23WHTKLT4_1
07:39:55 : INFO : Running: touch /tmp/nxf.Z1txKUq3z2/tih_rna_sample_00461_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok
07:39:55 : INFO : Running: samtools sort -o tih_rna_sample_00461_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00461_B23WHTKLT4_1.cancer_intron_reads.bam
07:39:56 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o tih_rna_sample_00461_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00461_B23WHTKLT4_1.cancer_intron_reads.bam
07:39:56 : INFO : Running: touch /tmp/nxf.Z1txKUq3z2/tih_rna_sample_00461_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok
07:39:56 : INFO : Running: samtools sort -o tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.bam tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.bam
[bam_sort_core] merging from 4 files and 1 in-memory blocks...
07:41:03 : INFO : Execution Time = 1.13 minutes. CMD: samtools sort -o tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.bam tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.bam
07:41:03 : INFO : Running: touch /tmp/nxf.Z1txKUq3z2/tih_rna_sample_00461_B23WHTKLT4_1.chckpts/sort_gene_reads.ok
07:41:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.bam
07:41:26 : INFO : Execution Time = 0.38 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.bam
07:41:26 : INFO : Running: touch /tmp/nxf.Z1txKUq3z2/tih_rna_sample_00461_B23WHTKLT4_1.chckpts/tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:41:26 : INFO : Running: samtools sort -o tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
07:41:32 : INFO : Execution Time = 0.10 minutes. CMD: samtools sort -o tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
07:41:32 : INFO : Running: touch /tmp/nxf.Z1txKUq3z2/tih_rna_sample_00461_B23WHTKLT4_1.chckpts/tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:41:32 : INFO : Running: samtools index tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
07:41:33 : INFO : Execution Time = 0.01 minutes. CMD: samtools index tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
07:41:33 : INFO : Running: touch /tmp/nxf.Z1txKUq3z2/tih_rna_sample_00461_B23WHTKLT4_1.chckpts/tih_rna_sample_00461_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:41:33 : INFO : Running: samtools index tih_rna_sample_00461_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
07:41:33 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00461_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
07:41:33 : INFO : Running: touch /tmp/nxf.Z1txKUq3z2/tih_rna_sample_00461_B23WHTKLT4_1.chckpts/tih_rna_sample_00461_B23WHTKLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:41:33 : INFO : Running: create_report tih_rna_sample_00461_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00461_B23WHTKLT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00461_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00461_B23WHTKLT4_1'
07:42:31 : INFO : Execution Time = 0.97 minutes. CMD: create_report tih_rna_sample_00461_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00461_B23WHTKLT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00461_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00461_B23WHTKLT4_1'
07:42:31 : INFO : Running: touch /tmp/nxf.Z1txKUq3z2/tih_rna_sample_00461_B23WHTKLT4_1.chckpts/igv_create_html.ok
07:42:31 : INFO : done.