07:32:51 : 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=12000000.00/min
[210000], rate=12600000.00/min
[220000], rate=13200000.00/min
[230000], rate=13800000.00/min
[240000], rate=14400000.00/min
[250000], rate=15000000.00/min
[260000], rate=15600000.00/min
[270000], rate=16200000.00/min
[280000], rate=16800000.00/min
[290000], rate=17400000.00/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=10800000.00/min
[370000], rate=11100000.00/min
[380000], rate=11400000.00/min
[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
[480000], rate=14400000.00/min
[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=16800000.00/min
[570000], rate=17100000.00/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
[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 07:32:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_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.
-1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 108 cancer introns
07:32:59 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim
07:32:59 : INFO : Running: touch /tmp/nxf.nWsFnAJ6BS/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok
07:32:59 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns
07:32:59 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns
07:32:59 : INFO : Running: touch /tmp/nxf.nWsFnAJ6BS/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok
07:32:59 : INFO : -found 60 cancer introns
07:32:59 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
07:32:59 : INFO : Creating the BED File.
07:33:00 : INFO : Saving Bed File as 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
07:33:00 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
07:33:00 : INFO : Running: touch /tmp/nxf.nWsFnAJ6BS/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok
07:33:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1
[W::hts_idx_load3] The index file is older than the data file: 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
07:33:05 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1
07:33:05 : INFO : Running: touch /tmp/nxf.nWsFnAJ6BS/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok
07:33:05 : INFO : Running: samtools sort -o 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
07:33:05 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
07:33:05 : INFO : Running: touch /tmp/nxf.nWsFnAJ6BS/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok
07:33:05 : INFO : Running: samtools sort -o 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
07:33:10 : INFO : Execution Time = 0.08 minutes. CMD: samtools sort -o 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
07:33:10 : INFO : Running: touch /tmp/nxf.nWsFnAJ6BS/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_gene_reads.ok
07:33:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam
07:33:12 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam
07:33:12 : INFO : Running: touch /tmp/nxf.nWsFnAJ6BS/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:33:12 : INFO : Running: samtools sort -o 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
07:33:12 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
07:33:12 : INFO : Running: touch /tmp/nxf.nWsFnAJ6BS/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:33:12 : INFO : Running: samtools index 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam
07:33:12 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam
07:33:12 : INFO : Running: touch /tmp/nxf.nWsFnAJ6BS/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:33:12 : INFO : Running: samtools index 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam
07:33:12 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam
07:33:12 : INFO : Running: touch /tmp/nxf.nWsFnAJ6BS/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:33:12 : INFO : Running: create_report 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1'
07:33:19 : INFO : Execution Time = 0.12 minutes. CMD: create_report 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1'
07:33:19 : INFO : Running: touch /tmp/nxf.nWsFnAJ6BS/1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/igv_create_html.ok
07:33:20 : INFO : done.