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rate=12977142.86/min [7580000], rate=12994285.71/min [7590000], rate=13011428.57/min [7600000], rate=13028571.43/min [7610000], rate=13045714.29/min [7620000], rate=13062857.14/min [7630000], rate=13080000.00/min [7640000], rate=13097142.86/min [7650000], rate=13114285.71/min [7660000], rate=13131428.57/min [7670000], rate=13148571.43/min [7680000], rate=13165714.29/min [7690000], rate=12816666.67/min [7700000], rate=12833333.33/min [7710000], rate=12850000.00/min [7720000], rate=12866666.67/min [7730000], rate=12883333.33/min [7740000], rate=12900000.00/min [7750000], rate=12916666.67/min [7760000], rate=12933333.33/min [7770000], rate=12950000.00/min [7780000], rate=12966666.67/min [7790000], rate=12983333.33/min [7800000], rate=13000000.00/min [7810000], rate=13016666.67/min [7820000], rate=13033333.33/min [7830000], rate=13050000.00/min [7840000], rate=13066666.67/min [7850000], rate=13083333.33/min [7860000], rate=13100000.00/min [7870000], rate=13116666.67/min [7880000], 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rate=12931578.95/min [8200000], rate=12947368.42/min [8210000], rate=12963157.89/min [8220000], rate=12978947.37/min [8230000], rate=12994736.84/min [8240000], rate=13010526.32/min [8250000], rate=13026315.79/min [8260000], rate=13042105.26/min [8270000], rate=13057894.74/min [8280000], rate=13073684.21/min [8290000], rate=13089473.68/min [8300000], rate=13105263.16/min [8310000], rate=13121052.63/min [8320000], rate=13136842.11/min [8330000], rate=13152631.58/min [8340000], rate=13168421.05/min [8350000], rate=13184210.53/min [8360000], rate=13200000.00/min [8370000], rate=13215789.47/min [8380000], rate=13231578.95/min [8390000], rate=13247368.42/min [8400000], rate=13263157.89/min [8410000], rate=12938461.54/min [8420000], rate=12953846.15/min [8430000], rate=12969230.77/min [8440000], rate=12984615.38/min [8450000], rate=13000000.00/min [8460000], rate=13015384.62/min [8470000], rate=13030769.23/min [8480000], rate=13046153.85/min [8490000], rate=13061538.46/min [8500000], rate=13076923.08/min [8510000], rate=13092307.69/min [8520000], rate=13107692.31/min [8530000], rate=13123076.92/min [8540000], rate=13138461.54/min [8550000], rate=13153846.15/min [8560000], rate=13169230.77/min [8570000], rate=13184615.38/min [8580000], rate=13200000.00/min [8590000], rate=13215384.62/min [8600000], rate=13230769.23/min [8610000], rate=13246153.85/min [8620000], rate=13261538.46/min [8630000], rate=13276923.08/min [8640000], rate=12960000.00/min [8650000], rate=12975000.00/min [8660000], rate=12990000.00/min [8670000], rate=13005000.00/min [8680000], rate=13020000.00/min [8690000], rate=13035000.00/min [8700000], rate=13050000.00/min [8710000], rate=13065000.00/min [8720000], rate=13080000.00/min [8730000], rate=13095000.00/min [8740000], rate=13110000.00/min [8750000], rate=13125000.00/min [8760000], rate=13140000.00/min [8770000], rate=13155000.00/min [8780000], rate=13170000.00/min [8790000], rate=13185000.00/min [8800000], rate=13200000.00/min [8810000], rate=13215000.00/min [8820000], rate=13230000.00/min [8830000], rate=13245000.00/min [8840000], rate=13260000.00/min [8850000], rate=13275000.00/min [8860000], rate=13290000.00/min [8870000], rate=13305000.00/min [8880000], rate=12995121.95/min [8890000], rate=13009756.10/min [8900000], rate=13024390.24/min [8910000], rate=13039024.39/min [8920000], rate=13053658.54/min [8930000], rate=13068292.68/min [8940000], rate=13082926.83/min [8950000], rate=13097560.98/min [8960000], rate=13112195.12/min [8970000], rate=13126829.27/min [8980000], rate=13141463.41/min [8990000], rate=13156097.56/min [9000000], rate=13170731.71/min [9010000], rate=13185365.85/min [9020000], rate=13200000.00/min [9030000], rate=13214634.15/min [9040000], rate=13229268.29/min [9050000], rate=13243902.44/min [9060000], rate=13258536.59/min [9070000], rate=13273170.73/min [9080000], rate=13287804.88/min [9090000], rate=13302439.02/min [9100000], rate=13317073.17/min [9110000], rate=13331707.32/min [9120000], rate=13346341.46/min [9130000], rate=13360975.61/min [9140000], rate=13057142.86/min [9150000], rate=13071428.57/min [9160000], rate=13085714.29/min [9170000], rate=13100000.00/min [9180000], rate=13114285.71/min [9190000], rate=13128571.43/min [9200000], rate=13142857.14/min [9210000], rate=13157142.86/min [9220000], rate=13171428.57/min [9230000], rate=13185714.29/min [9240000], rate=13200000.00/min [9250000], rate=13214285.71/min [9260000], rate=13228571.43/min [9270000], rate=13242857.14/min [9280000], rate=13257142.86/min [9290000], rate=13271428.57/min [9300000], rate=13285714.29/min [9310000], rate=13300000.00/min [9320000], rate=13314285.71/min [9330000], rate=13328571.43/min [9340000], rate=13342857.14/min [9350000], rate=13357142.86/min [9360000], rate=13371428.57/min [9370000], rate=13385714.29/min [9380000], rate=13400000.00/min [9390000], rate=13414285.71/min [9400000], rate=13428571.43/min [9410000], rate=13442857.14/min [9420000], rate=13144186.05/min [9430000], rate=13158139.53/min 20:49:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-01eb49-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-01eb49-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-01eb49-R1_A23YTGFLT4_1.introns: identified 7711 cancer introns 20:49:08 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-01eb49-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer.introns.prelim 20:49:08 : INFO : Running: touch /tmp/nxf.4xHqbF43UZ/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 20:49:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer.introns 20:49:08 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer.introns 20:49:08 : INFO : Running: touch /tmp/nxf.4xHqbF43UZ/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 20:49:08 : INFO : -found 2833 cancer introns 20:49:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-01eb49-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-01eb49-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:49:09 : INFO : Creating the BED File. 20:49:19 : INFO : Saving Bed File as aih-tih-sc-01eb49-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:49:20 : INFO : Execution Time = 0.19 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-01eb49-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-01eb49-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:49:20 : INFO : Running: touch /tmp/nxf.4xHqbF43UZ/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 20:49:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-01eb49-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-01eb49-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-01eb49-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01eb49-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 21:19:53 : INFO : Execution Time = 30.56 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-01eb49-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-01eb49-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-01eb49-R1_A23YTGFLT4_1 21:19:53 : INFO : Running: touch /tmp/nxf.4xHqbF43UZ/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 21:19:53 : INFO : Running: samtools sort -o aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer_intron_reads.bam 21:19:53 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer_intron_reads.bam 21:19:53 : INFO : Running: touch /tmp/nxf.4xHqbF43UZ/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 21:19:53 : INFO : Running: samtools sort -o aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 140 files and 1 in-memory blocks... 21:53:00 : INFO : Execution Time = 33.10 minutes. CMD: samtools sort -o aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.bam 21:53:00 : INFO : Running: touch /tmp/nxf.4xHqbF43UZ/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok 21:53:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.bam 22:01:39 : INFO : Execution Time = 8.65 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.bam 22:01:39 : INFO : Running: touch /tmp/nxf.4xHqbF43UZ/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 22:01:39 : INFO : Running: samtools sort -o aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 22:02:37 : INFO : Execution Time = 0.97 minutes. CMD: samtools sort -o aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp 22:02:37 : INFO : Running: touch /tmp/nxf.4xHqbF43UZ/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 22:02:37 : INFO : Running: samtools index aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 22:02:44 : INFO : Execution Time = 0.11 minutes. CMD: samtools index aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 22:02:44 : INFO : Running: touch /tmp/nxf.4xHqbF43UZ/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 22:02:44 : INFO : Running: samtools index aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 22:02:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 22:02:44 : INFO : Running: touch /tmp/nxf.4xHqbF43UZ/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 22:02:44 : INFO : Running: create_report aih-tih-sc-01eb49-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-01eb49-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-01eb49-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-01eb49-R1_A23YTGFLT4_1' 22:09:49 : INFO : Execution Time = 7.09 minutes. CMD: create_report aih-tih-sc-01eb49-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-01eb49-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-01eb49-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-01eb49-R1_A23YTGFLT4_1' 22:09:49 : INFO : Running: touch /tmp/nxf.4xHqbF43UZ/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok 22:09:49 : INFO : done.