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rate=25960000.00/min [6500000], rate=26000000.00/min [6510000], rate=26040000.00/min [6520000], rate=26080000.00/min [6530000], rate=26120000.00/min [6540000], rate=26160000.00/min [6550000], rate=26200000.00/min [6560000], rate=26240000.00/min [6570000], rate=26280000.00/min [6580000], rate=26320000.00/min [6590000], rate=26360000.00/min [6600000], rate=26400000.00/min [6610000], rate=26440000.00/min [6620000], rate=26480000.00/min [6630000], rate=26520000.00/min [6640000], rate=26560000.00/min [6650000], rate=26600000.00/min [6660000], rate=26640000.00/min [6670000], rate=26680000.00/min [6680000], rate=26720000.00/min [6690000], rate=26760000.00/min [6700000], rate=26800000.00/min [6710000], rate=26840000.00/min [6720000], rate=26880000.00/min [6730000], rate=26920000.00/min [6740000], rate=26960000.00/min [6750000], rate=27000000.00/min [6760000], rate=27040000.00/min [6770000], rate=27080000.00/min [6780000], rate=27120000.00/min [6790000], rate=27160000.00/min [6800000], rate=27200000.00/min [6810000], rate=27240000.00/min [6820000], rate=27280000.00/min [6830000], rate=27320000.00/min [6840000], rate=27360000.00/min [6850000], rate=27400000.00/min [6860000], rate=27440000.00/min [6870000], rate=25762500.00/min [6880000], rate=25800000.00/min [6890000], rate=25837500.00/min [6900000], rate=25875000.00/min [6910000], rate=25912500.00/min [6920000], rate=25950000.00/min [6930000], rate=25987500.00/min [6940000], rate=26025000.00/min [6950000], rate=26062500.00/min [6960000], rate=26100000.00/min [6970000], rate=26137500.00/min [6980000], rate=26175000.00/min [6990000], rate=26212500.00/min [7000000], rate=26250000.00/min [7010000], rate=26287500.00/min [7020000], rate=26325000.00/min [7030000], rate=26362500.00/min [7040000], rate=26400000.00/min [7050000], rate=26437500.00/min [7060000], rate=26475000.00/min [7070000], rate=26512500.00/min [7080000], rate=26550000.00/min [7090000], rate=26587500.00/min [7100000], rate=26625000.00/min [7110000], rate=26662500.00/min [7120000], rate=26700000.00/min [7130000], rate=26737500.00/min [7140000], rate=26775000.00/min [7150000], rate=26812500.00/min [7160000], rate=26850000.00/min [7170000], rate=26887500.00/min [7180000], rate=25341176.47/min [7190000], rate=25376470.59/min [7200000], rate=25411764.71/min [7210000], rate=25447058.82/min [7220000], rate=25482352.94/min [7230000], rate=25517647.06/min [7240000], rate=25552941.18/min [7250000], rate=25588235.29/min [7260000], rate=25623529.41/min [7270000], rate=25658823.53/min [7280000], rate=25694117.65/min [7290000], rate=25729411.76/min [7300000], rate=25764705.88/min [7310000], rate=25800000.00/min [7320000], rate=25835294.12/min [7330000], rate=25870588.24/min [7340000], rate=25905882.35/min [7350000], rate=25941176.47/min [7360000], rate=25976470.59/min [7370000], rate=26011764.71/min [7380000], rate=26047058.82/min [7390000], rate=26082352.94/min [7400000], rate=26117647.06/min [7410000], rate=26152941.18/min [7420000], rate=26188235.29/min [7430000], rate=26223529.41/min [7440000], rate=26258823.53/min [7450000], rate=26294117.65/min [7460000], rate=26329411.76/min [7470000], rate=26364705.88/min [7480000], rate=26400000.00/min [7490000], rate=24966666.67/min [7500000], rate=25000000.00/min [7510000], rate=25033333.33/min [7520000], rate=25066666.67/min [7530000], rate=25100000.00/min [7540000], rate=25133333.33/min [7550000], rate=25166666.67/min [7560000], rate=25200000.00/min [7570000], rate=25233333.33/min [7580000], rate=25266666.67/min [7590000], rate=25300000.00/min [7600000], rate=25333333.33/min [7610000], rate=25366666.67/min [7620000], rate=25400000.00/min [7630000], rate=25433333.33/min [7640000], rate=25466666.67/min [7650000], rate=25500000.00/min [7660000], rate=25533333.33/min [7670000], rate=25566666.67/min [7680000], rate=25600000.00/min [7690000], rate=25633333.33/min [7700000], rate=25666666.67/min [7710000], rate=25700000.00/min [7720000], rate=25733333.33/min [7730000], rate=25766666.67/min [7740000], rate=25800000.00/min [7750000], rate=25833333.33/min [7760000], rate=25866666.67/min [7770000], rate=25900000.00/min [7780000], rate=25933333.33/min [7790000], rate=25966666.67/min [7800000], rate=26000000.00/min [7810000], rate=26033333.33/min [7820000], rate=26066666.67/min [7830000], rate=26100000.00/min [7840000], rate=26133333.33/min [7850000], rate=26166666.67/min [7860000], rate=26200000.00/min [7870000], rate=26233333.33/min [7880000], rate=26266666.67/min [7890000], rate=26300000.00/min [7900000], rate=26333333.33/min [7910000], rate=26366666.67/min [7920000], rate=26400000.00/min [7930000], rate=26433333.33/min [7940000], rate=25073684.21/min [7950000], rate=25105263.16/min [7960000], rate=25136842.11/min [7970000], rate=25168421.05/min [7980000], rate=25200000.00/min [7990000], rate=25231578.95/min [8000000], rate=25263157.89/min [8010000], rate=25294736.84/min [8020000], rate=25326315.79/min [8030000], rate=25357894.74/min [8040000], rate=25389473.68/min [8050000], rate=25421052.63/min [8060000], rate=25452631.58/min [8070000], rate=25484210.53/min [8080000], rate=25515789.47/min [8090000], rate=25547368.42/min [8100000], rate=25578947.37/min [8110000], rate=25610526.32/min [8120000], rate=25642105.26/min [8130000], rate=25673684.21/min [8140000], rate=25705263.16/min [8150000], rate=25736842.11/min [8160000], rate=25768421.05/min [8170000], rate=25800000.00/min [8180000], rate=25831578.95/min [8190000], rate=25863157.89/min [8200000], rate=25894736.84/min [8210000], rate=25926315.79/min [8220000], rate=25957894.74/min [8230000], rate=25989473.68/min [8240000], rate=26021052.63/min [8250000], rate=26052631.58/min [8260000], rate=26084210.53/min [8270000], rate=26115789.47/min [8280000], rate=26147368.42/min [8290000], rate=26178947.37/min [8300000], rate=26210526.32/min 08:14:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-31d31f-R1_A23YTGFLT4_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. -aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns: identified 2429 cancer introns 08:14:05 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer.introns.prelim 08:14:05 : INFO : Running: touch /tmp/nxf.aLFDLMkET3/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 08:14:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer.introns 08:14:05 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer.introns 08:14:05 : INFO : Running: touch /tmp/nxf.aLFDLMkET3/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 08:14:05 : INFO : -found 1436 cancer introns 08:14:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:14:05 : INFO : Creating the BED File. 08:14:08 : INFO : Saving Bed File as aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:14:08 : INFO : Execution Time = 0.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:14:08 : INFO : Running: touch /tmp/nxf.aLFDLMkET3/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 08:14:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-31d31f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-31d31f-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 08:22:36 : INFO : Execution Time = 8.46 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-31d31f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-31d31f-R1_A23YTGFLT4_1 08:22:36 : INFO : Running: touch /tmp/nxf.aLFDLMkET3/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 08:22:36 : INFO : Running: samtools sort -o aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer_intron_reads.bam 08:22:36 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer_intron_reads.bam 08:22:36 : INFO : Running: touch /tmp/nxf.aLFDLMkET3/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 08:22:36 : INFO : Running: samtools sort -o aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 54 files and 1 in-memory blocks... 08:33:43 : INFO : Execution Time = 11.11 minutes. CMD: samtools sort -o aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.bam 08:33:43 : INFO : Running: touch /tmp/nxf.aLFDLMkET3/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok 08:33:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.bam 08:37:26 : INFO : Execution Time = 3.72 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.bam 08:37:26 : INFO : Running: touch /tmp/nxf.aLFDLMkET3/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 08:37:26 : INFO : Running: samtools sort -o aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 1 files and 1 in-memory blocks... 08:37:50 : INFO : Execution Time = 0.41 minutes. CMD: samtools sort -o aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp 08:37:50 : INFO : Running: touch /tmp/nxf.aLFDLMkET3/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 08:37:50 : INFO : Running: samtools index aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 08:37:53 : INFO : Execution Time = 0.04 minutes. CMD: samtools index aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 08:37:53 : INFO : Running: touch /tmp/nxf.aLFDLMkET3/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 08:37:53 : INFO : Running: samtools index aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 08:37:53 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 08:37:53 : INFO : Running: touch /tmp/nxf.aLFDLMkET3/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 08:37:53 : INFO : Running: create_report aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-31d31f-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-31d31f-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-31d31f-R1_A23YTGFLT4_1' 08:40:17 : INFO : Execution Time = 2.40 minutes. CMD: create_report aih-tih-sc-31d31f-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-31d31f-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-31d31f-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-31d31f-R1_A23YTGFLT4_1' 08:40:17 : INFO : Running: touch /tmp/nxf.aLFDLMkET3/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok 08:40:17 : INFO : done.