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 [50000], rate=3000000.00/min [60000], rate=3600000.00/min [70000], rate=4200000.00/min [80000], rate=4800000.00/min [90000], rate=5400000.00/min [100000], rate=6000000.00/min [110000], rate=6600000.00/min [120000], rate=7200000.00/min [130000], rate=7800000.00/min [140000], rate=8400000.00/min [150000], rate=9000000.00/min [160000], rate=9600000.00/min [170000], rate=10200000.00/min [180000], rate=10800000.00/min [190000], rate=11400000.00/min [200000], rate=6000000.00/min [210000], rate=6300000.00/min [220000], rate=6600000.00/min [230000], rate=6900000.00/min [240000], rate=7200000.00/min [250000], rate=7500000.00/min [260000], rate=7800000.00/min [270000], rate=8100000.00/min [280000], rate=8400000.00/min [290000], rate=8700000.00/min [300000], rate=9000000.00/min [310000], rate=9300000.00/min [320000], rate=9600000.00/min [330000], rate=9900000.00/min [340000], rate=10200000.00/min [350000], rate=10500000.00/min [360000], rate=7200000.00/min [370000], rate=7400000.00/min [380000], rate=7600000.00/min [390000], rate=7800000.00/min [400000], rate=8000000.00/min [410000], rate=8200000.00/min [420000], rate=8400000.00/min [430000], rate=8600000.00/min [440000], rate=8800000.00/min [450000], rate=9000000.00/min [460000], rate=9200000.00/min [470000], rate=9400000.00/min [480000], rate=9600000.00/min [490000], rate=9800000.00/min [500000], rate=7500000.00/min [510000], rate=7650000.00/min [520000], rate=7800000.00/min [530000], rate=7950000.00/min [540000], rate=8100000.00/min [550000], rate=8250000.00/min [560000], rate=8400000.00/min [570000], rate=8550000.00/min [580000], rate=8700000.00/min [590000], rate=8850000.00/min [600000], rate=9000000.00/min [610000], rate=9150000.00/min [620000], rate=9300000.00/min [630000], rate=9450000.00/min [640000], rate=9600000.00/min [650000], rate=9750000.00/min [660000], rate=9900000.00/min [670000], rate=10050000.00/min [680000], rate=10200000.00/min [690000], rate=10350000.00/min [700000], rate=8400000.00/min [710000], rate=8520000.00/min [720000], rate=8640000.00/min [730000], rate=8760000.00/min [740000], rate=8880000.00/min [750000], rate=9000000.00/min [760000], rate=9120000.00/min [770000], rate=9240000.00/min [780000], rate=9360000.00/min [790000], rate=9480000.00/min [800000], rate=9600000.00/min [810000], rate=9720000.00/min [820000], rate=9840000.00/min [830000], rate=9960000.00/min [840000], rate=10080000.00/min [850000], rate=10200000.00/min [860000], rate=10320000.00/min [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 [950000], rate=9500000.00/min [960000], rate=9600000.00/min [970000], rate=9700000.00/min [980000], rate=9800000.00/min [990000], rate=9900000.00/min [1000000], rate=10000000.00/min [1010000], rate=10100000.00/min [1020000], rate=10200000.00/min [1030000], rate=8828571.43/min [1040000], rate=8914285.71/min [1050000], rate=9000000.00/min [1060000], rate=9085714.29/min [1070000], rate=9171428.57/min [1080000], rate=9257142.86/min [1090000], rate=9342857.14/min [1100000], rate=9428571.43/min [1110000], rate=9514285.71/min [1120000], rate=9600000.00/min [1130000], rate=9685714.29/min [1140000], rate=9771428.57/min [1150000], rate=9857142.86/min [1160000], rate=9942857.14/min [1170000], rate=10028571.43/min [1180000], rate=10114285.71/min [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 [1270000], rate=9525000.00/min [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 [1330000], rate=9975000.00/min [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.