07:27:22 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[120000], rate=7200000.00/min
[130000], rate=7800000.00/min
[140000], rate=8400000.00/min
[150000], rate=9000000.00/min
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[210000], rate=12600000.00/min
[220000], rate=13200000.00/min
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[250000], rate=15000000.00/min
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[270000], rate=16200000.00/min
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[300000], rate=18000000.00/min
[310000], rate=18600000.00/min
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[340000], rate=10200000.00/min
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[370000], rate=11100000.00/min
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[390000], rate=11700000.00/min
[400000], rate=12000000.00/min
[410000], rate=12300000.00/min
[420000], rate=12600000.00/min
[430000], rate=12900000.00/min
[440000], rate=13200000.00/min
[450000], rate=13500000.00/min
[460000], rate=13800000.00/min
[470000], rate=14100000.00/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
[540000], rate=16200000.00/min
[550000], rate=16500000.00/min
[560000], rate=11200000.00/min
[570000], rate=11400000.00/min
[580000], rate=11600000.00/min
[590000], rate=11800000.00/min
[600000], rate=12000000.00/min
[610000], rate=12200000.00/min
[620000], rate=12400000.00/min
[630000], rate=12600000.00/min
[640000], rate=12800000.00/min
[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
[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=11850000.00/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
[930000], rate=13950000.00/min
[940000], rate=14100000.00/min
[950000], rate=14250000.00/min
[960000], rate=14400000.00/min
[970000], rate=14550000.00/min
[980000], rate=11760000.00/min
[990000], rate=11880000.00/min
[1000000], rate=12000000.00/min
[1010000], rate=12120000.00/min
[1020000], rate=12240000.00/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
[1100000], rate=13200000.00/min
[1110000], rate=13320000.00/min
[1120000], rate=13440000.00/min
[1130000], rate=13560000.00/min
[1140000], rate=13680000.00/min
[1150000], rate=13800000.00/min
[1160000], rate=11600000.00/min
[1170000], rate=11700000.00/min
[1180000], rate=11800000.00/min
[1190000], rate=11900000.00/min
[1200000], rate=12000000.00/min
[1210000], rate=12100000.00/min
[1220000], rate=12200000.00/min
[1230000], rate=12300000.00/min
[1240000], rate=12400000.00/min
[1250000], rate=12500000.00/min
[1260000], rate=12600000.00/min
[1270000], rate=12700000.00/min
[1280000], rate=12800000.00/min
[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=11914285.71/min
[1400000], rate=12000000.00/min
[1410000], rate=12085714.29/min
[1420000], rate=12171428.57/min
[1430000], rate=12257142.86/min
[1440000], rate=12342857.14/min
[1450000], rate=12428571.43/min
[1460000], rate=12514285.71/min
[1470000], rate=12600000.00/min
[1480000], rate=12685714.29/min
[1490000], rate=12771428.57/min
[1500000], rate=12857142.86/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=12225000.00/min
[1640000], rate=12300000.00/min
[1650000], rate=12375000.00/min
[1660000], rate=12450000.00/min
[1670000], rate=12525000.00/min
[1680000], rate=12600000.00/min 07:27:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > ColoN_FFPE_L06_RNA_01_B23LG7FLT4_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.
-ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns: identified 91 cancer introns
07:27:38 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer.introns.prelim
07:27:38 : INFO : Running: touch /tmp/nxf.1sBbJwBw1C/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok
07:27:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer.introns
07:27:38 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer.introns
07:27:38 : INFO : Running: touch /tmp/nxf.1sBbJwBw1C/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok
07:27:38 : INFO : -found 39 cancer introns
07:27:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns --cancer_introns ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
07:27:39 : INFO : Creating the BED File.
07:27:39 : INFO : Saving Bed File as ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
07:27:39 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns --cancer_introns ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
07:27:39 : INFO : Running: touch /tmp/nxf.1sBbJwBw1C/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
07:27:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1
[W::hts_idx_load3] The index file is older than the data file: ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
07:27:40 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1
07:27:40 : INFO : Running: touch /tmp/nxf.1sBbJwBw1C/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
07:27:41 : INFO : Running: samtools sort -o ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
07:27:41 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
07:27:41 : INFO : Running: touch /tmp/nxf.1sBbJwBw1C/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
07:27:41 : INFO : Running: samtools sort -o ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.bam
07:27:41 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.bam
07:27:41 : INFO : Running: touch /tmp/nxf.1sBbJwBw1C/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
07:27:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam
07:27:42 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam
07:27:42 : INFO : Running: touch /tmp/nxf.1sBbJwBw1C/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.chckpts/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:27:42 : INFO : Running: samtools sort -o ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
07:27:42 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
07:27:42 : INFO : Running: touch /tmp/nxf.1sBbJwBw1C/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.chckpts/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:27:42 : INFO : Running: samtools index ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
07:27:42 : INFO : Execution Time = 0.00 minutes. CMD: samtools index ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
07:27:42 : INFO : Running: touch /tmp/nxf.1sBbJwBw1C/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.chckpts/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:27:42 : INFO : Running: samtools index ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
07:27:42 : INFO : Execution Time = 0.00 minutes. CMD: samtools index ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
07:27:42 : INFO : Running: touch /tmp/nxf.1sBbJwBw1C/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.chckpts/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:27:42 : INFO : Running: create_report ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1'
07:27:47 : INFO : Execution Time = 0.07 minutes. CMD: create_report ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1'
07:27:47 : INFO : Running: touch /tmp/nxf.1sBbJwBw1C/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok
07:27:47 : INFO : done.