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rate=12972413.79/min [6280000], rate=12993103.45/min [6290000], rate=13013793.10/min [6300000], rate=13034482.76/min [6310000], rate=13055172.41/min [6320000], rate=13075862.07/min [6330000], rate=13096551.72/min [6340000], rate=13117241.38/min [6350000], rate=12700000.00/min [6360000], rate=12720000.00/min [6370000], rate=12740000.00/min [6380000], rate=12760000.00/min [6390000], rate=12780000.00/min [6400000], rate=12800000.00/min [6410000], rate=12820000.00/min [6420000], rate=12840000.00/min [6430000], rate=12860000.00/min [6440000], rate=12880000.00/min [6450000], rate=12900000.00/min [6460000], rate=12920000.00/min [6470000], rate=12940000.00/min [6480000], rate=12960000.00/min [6490000], rate=12980000.00/min [6500000], rate=13000000.00/min [6510000], rate=13020000.00/min [6520000], rate=13040000.00/min [6530000], rate=13060000.00/min [6540000], rate=13080000.00/min [6550000], rate=13100000.00/min [6560000], rate=13120000.00/min [6570000], rate=13140000.00/min [6580000], rate=13160000.00/min [6590000], rate=13180000.00/min [6600000], rate=12774193.55/min [6610000], rate=12793548.39/min [6620000], rate=12812903.23/min [6630000], rate=12832258.06/min [6640000], rate=12851612.90/min [6650000], rate=12870967.74/min [6660000], rate=12890322.58/min [6670000], rate=12909677.42/min [6680000], rate=12929032.26/min [6690000], rate=12948387.10/min [6700000], rate=12967741.94/min [6710000], rate=12987096.77/min [6720000], rate=13006451.61/min [6730000], rate=13025806.45/min [6740000], rate=13045161.29/min [6750000], rate=13064516.13/min [6760000], rate=13083870.97/min [6770000], rate=13103225.81/min [6780000], rate=13122580.65/min [6790000], rate=13141935.48/min [6800000], rate=13161290.32/min [6810000], rate=13180645.16/min [6820000], rate=13200000.00/min [6830000], rate=13219354.84/min [6840000], rate=13238709.68/min [6850000], rate=12843750.00/min [6860000], rate=12862500.00/min [6870000], rate=12881250.00/min [6880000], rate=12900000.00/min [6890000], rate=12918750.00/min [6900000], rate=12937500.00/min [6910000], rate=12956250.00/min [6920000], rate=12975000.00/min [6930000], rate=12993750.00/min [6940000], rate=13012500.00/min [6950000], rate=13031250.00/min [6960000], rate=13050000.00/min [6970000], rate=13068750.00/min [6980000], rate=13087500.00/min [6990000], rate=13106250.00/min [7000000], rate=13125000.00/min [7010000], rate=13143750.00/min [7020000], rate=13162500.00/min [7030000], rate=13181250.00/min [7040000], rate=13200000.00/min [7050000], rate=13218750.00/min [7060000], rate=13237500.00/min [7070000], rate=13256250.00/min [7080000], rate=13275000.00/min [7090000], rate=12890909.09/min [7100000], rate=12909090.91/min [7110000], rate=12927272.73/min [7120000], rate=12945454.55/min [7130000], rate=12963636.36/min [7140000], rate=12981818.18/min [7150000], rate=13000000.00/min [7160000], rate=13018181.82/min [7170000], rate=13036363.64/min [7180000], rate=13054545.45/min [7190000], rate=13072727.27/min [7200000], rate=13090909.09/min [7210000], rate=13109090.91/min [7220000], rate=13127272.73/min [7230000], rate=13145454.55/min [7240000], rate=13163636.36/min [7250000], rate=13181818.18/min [7260000], rate=13200000.00/min [7270000], rate=13218181.82/min [7280000], rate=13236363.64/min [7290000], rate=12864705.88/min [7300000], rate=12882352.94/min [7310000], rate=12900000.00/min [7320000], rate=12917647.06/min [7330000], rate=12935294.12/min [7340000], rate=12952941.18/min [7350000], rate=12970588.24/min [7360000], rate=12988235.29/min [7370000], rate=13005882.35/min [7380000], rate=13023529.41/min [7390000], rate=13041176.47/min [7400000], rate=13058823.53/min [7410000], rate=13076470.59/min [7420000], rate=13094117.65/min [7430000], rate=13111764.71/min [7440000], rate=13129411.76/min [7450000], rate=13147058.82/min [7460000], rate=13164705.88/min [7470000], rate=13182352.94/min [7480000], rate=13200000.00/min [7490000], rate=13217647.06/min [7500000], rate=13235294.12/min [7510000], rate=13252941.18/min [7520000], rate=13270588.24/min [7530000], rate=13288235.29/min [7540000], rate=12925714.29/min [7550000], rate=12942857.14/min [7560000], rate=12960000.00/min [7570000], 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=13182857.14/min [7700000], rate=13200000.00/min [7710000], rate=13217142.86/min [7720000], rate=13234285.71/min [7730000], rate=13251428.57/min [7740000], rate=13268571.43/min [7750000], rate=13285714.29/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], rate=13133333.33/min [7890000], rate=13150000.00/min [7900000], rate=13166666.67/min [7910000], rate=13183333.33/min [7920000], rate=13200000.00/min [7930000], rate=13216666.67/min [7940000], rate=13233333.33/min [7950000], rate=13250000.00/min [7960000], rate=13266666.67/min [7970000], rate=13283333.33/min [7980000], rate=13300000.00/min [7990000], rate=13316666.67/min [8000000], rate=13333333.33/min [8010000], rate=12989189.19/min [8020000], rate=13005405.41/min [8030000], rate=13021621.62/min [8040000], rate=13037837.84/min [8050000], rate=13054054.05/min [8060000], rate=13070270.27/min [8070000], rate=13086486.49/min [8080000], rate=13102702.70/min [8090000], rate=13118918.92/min [8100000], rate=13135135.14/min [8110000], rate=13151351.35/min [8120000], rate=13167567.57/min [8130000], rate=13183783.78/min [8140000], rate=13200000.00/min [8150000], rate=13216216.22/min [8160000], rate=13232432.43/min [8170000], rate=13248648.65/min [8180000], rate=13264864.86/min [8190000], rate=13281081.08/min [8200000], rate=13297297.30/min [8210000], rate=13313513.51/min [8220000], rate=13329729.73/min [8230000], rate=13345945.95/min [8240000], rate=13362162.16/min [8250000], rate=13378378.38/min [8260000], rate=13394594.59/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 08:50:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00419_23H5VFLT4_s44.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00419_23H5VFLT4_s44.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_00419_23H5VFLT4_s44.introns: identified 7888 cancer introns 08:50:42 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00419_23H5VFLT4_s44.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00419_23H5VFLT4_s44.cancer.introns.prelim 08:50:42 : INFO : Running: touch /tmp/nxf.h1Zx6NoucY/tih_rna_sample_00419_23H5VFLT4_s44.chckpts/prelim_introns.ok 08:50:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00419_23H5VFLT4_s44.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00419_23H5VFLT4_s44.cancer.introns 08:50:43 : 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_00419_23H5VFLT4_s44.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00419_23H5VFLT4_s44.cancer.introns 08:50:43 : INFO : Running: touch /tmp/nxf.h1Zx6NoucY/tih_rna_sample_00419_23H5VFLT4_s44.chckpts/introns_filtered.ok 08:50:43 : INFO : -found 3419 cancer introns 08:50:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00419_23H5VFLT4_s44.introns --cancer_introns tih_rna_sample_00419_23H5VFLT4_s44.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00419_23H5VFLT4_s44.introns.for_IGV.bed 08:50:43 : INFO : Creating the BED File. 08:50:51 : INFO : Saving Bed File as tih_rna_sample_00419_23H5VFLT4_s44.introns.for_IGV.bed 08:50:51 : INFO : Execution Time = 0.13 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00419_23H5VFLT4_s44.introns --cancer_introns tih_rna_sample_00419_23H5VFLT4_s44.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00419_23H5VFLT4_s44.introns.for_IGV.bed 08:50:51 : INFO : Running: touch /tmp/nxf.h1Zx6NoucY/tih_rna_sample_00419_23H5VFLT4_s44.chckpts/intron_igv_bed.ok 08:50:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00419_23H5VFLT4_s44.introns.for_IGV.bed --bam tih_rna_sample_00419_23H5VFLT4_s44.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00419_23H5VFLT4_s44 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00419_23H5VFLT4_s44.Aligned.sortedByCoord.out.bam.bai 09:16:09 : INFO : Execution Time = 25.30 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00419_23H5VFLT4_s44.introns.for_IGV.bed --bam tih_rna_sample_00419_23H5VFLT4_s44.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00419_23H5VFLT4_s44 09:16:09 : INFO : Running: touch /tmp/nxf.h1Zx6NoucY/tih_rna_sample_00419_23H5VFLT4_s44.chckpts/reads_alignments_extracted.ok 09:16:09 : INFO : Running: samtools sort -o tih_rna_sample_00419_23H5VFLT4_s44.cancer_intron_reads.sorted.bam tih_rna_sample_00419_23H5VFLT4_s44.cancer_intron_reads.bam 09:16:10 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00419_23H5VFLT4_s44.cancer_intron_reads.sorted.bam tih_rna_sample_00419_23H5VFLT4_s44.cancer_intron_reads.bam 09:16:10 : INFO : Running: touch /tmp/nxf.h1Zx6NoucY/tih_rna_sample_00419_23H5VFLT4_s44.chckpts/sort_cancer_intron_reads.ok 09:16:10 : INFO : Running: samtools sort -o tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.bam tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.bam [bam_sort_core] merging from 117 files and 1 in-memory blocks... 09:44:12 : INFO : Execution Time = 28.03 minutes. CMD: samtools sort -o tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.bam tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.bam 09:44:12 : INFO : Running: touch /tmp/nxf.h1Zx6NoucY/tih_rna_sample_00419_23H5VFLT4_s44.chckpts/sort_gene_reads.ok 09:44:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.bam 09:53:41 : INFO : Execution Time = 9.49 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.bam 09:53:41 : INFO : Running: touch /tmp/nxf.h1Zx6NoucY/tih_rna_sample_00419_23H5VFLT4_s44.chckpts/tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.sifted.bam.tmp.ok 09:53:41 : INFO : Running: samtools sort -o tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.sifted.bam tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 8 files and 1 in-memory blocks... 09:56:00 : INFO : Execution Time = 2.32 minutes. CMD: samtools sort -o tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.sifted.bam tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.sifted.bam.tmp 09:56:00 : INFO : Running: touch /tmp/nxf.h1Zx6NoucY/tih_rna_sample_00419_23H5VFLT4_s44.chckpts/tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:56:00 : INFO : Running: samtools index tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.sifted.bam 09:56:15 : INFO : Execution Time = 0.25 minutes. CMD: samtools index tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.sifted.bam 09:56:15 : INFO : Running: touch /tmp/nxf.h1Zx6NoucY/tih_rna_sample_00419_23H5VFLT4_s44.chckpts/tih_rna_sample_00419_23H5VFLT4_s44.gene_reads.sorted.sifted.bam.indexed.ok 09:56:15 : INFO : Running: samtools index tih_rna_sample_00419_23H5VFLT4_s44.cancer_intron_reads.sorted.bam 09:56:15 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00419_23H5VFLT4_s44.cancer_intron_reads.sorted.bam 09:56:15 : INFO : Running: touch /tmp/nxf.h1Zx6NoucY/tih_rna_sample_00419_23H5VFLT4_s44.chckpts/tih_rna_sample_00419_23H5VFLT4_s44.cancer_intron_reads.sorted.bam.indexed.ok 09:56:15 : INFO : Running: create_report tih_rna_sample_00419_23H5VFLT4_s44.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00419_23H5VFLT4_s44.ctat-splicing.igv.html --track-config tih_rna_sample_00419_23H5VFLT4_s44.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00419_23H5VFLT4_s44' 10:04:47 : INFO : Execution Time = 8.52 minutes. CMD: create_report tih_rna_sample_00419_23H5VFLT4_s44.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00419_23H5VFLT4_s44.ctat-splicing.igv.html --track-config tih_rna_sample_00419_23H5VFLT4_s44.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00419_23H5VFLT4_s44' 10:04:47 : INFO : Running: touch /tmp/nxf.h1Zx6NoucY/tih_rna_sample_00419_23H5VFLT4_s44.chckpts/igv_create_html.ok 10:04:47 : INFO : done.