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rate=31554545.45/min [11580000], rate=31581818.18/min [11590000], rate=31609090.91/min [11600000], rate=31636363.64/min [11610000], rate=31663636.36/min [11620000], rate=31690909.09/min [11630000], rate=31718181.82/min [11640000], rate=31745454.55/min [11650000], rate=31772727.27/min [11660000], rate=31800000.00/min [11670000], rate=31827272.73/min [11680000], rate=31854545.45/min [11690000], rate=31881818.18/min [11700000], rate=31909090.91/min [11710000], rate=31936363.64/min [11720000], rate=31963636.36/min [11730000], rate=31990909.09/min [11740000], rate=32018181.82/min [11750000], rate=32045454.55/min [11760000], rate=32072727.27/min [11770000], rate=32100000.00/min [11780000], rate=32127272.73/min [11790000], rate=32154545.45/min [11800000], rate=32181818.18/min [11810000], rate=32209090.91/min [11820000], rate=32236363.64/min [11830000], rate=32263636.36/min [11840000], rate=32290909.09/min [11850000], rate=32318181.82/min [11860000], rate=30939130.43/min [11870000], rate=30965217.39/min [11880000], rate=30991304.35/min [11890000], rate=31017391.30/min [11900000], rate=31043478.26/min [11910000], rate=31069565.22/min [11920000], rate=31095652.17/min [11930000], rate=31121739.13/min [11940000], rate=31147826.09/min [11950000], rate=31173913.04/min [11960000], rate=31200000.00/min [11970000], rate=31226086.96/min [11980000], rate=31252173.91/min [11990000], rate=31278260.87/min [12000000], rate=31304347.83/min [12010000], rate=31330434.78/min [12020000], rate=31356521.74/min [12030000], rate=31382608.70/min [12040000], rate=31408695.65/min [12050000], rate=31434782.61/min [12060000], rate=31460869.57/min [12070000], rate=31486956.52/min [12080000], rate=31513043.48/min [12090000], rate=31539130.43/min [12100000], rate=31565217.39/min [12110000], rate=31591304.35/min [12120000], rate=31617391.30/min [12130000], rate=31643478.26/min [12140000], rate=31669565.22/min [12150000], rate=31695652.17/min [12160000], rate=31721739.13/min [12170000], rate=31747826.09/min [12180000], rate=31773913.04/min [12190000], rate=31800000.00/min [12200000], rate=31826086.96/min [12210000], rate=31852173.91/min [12220000], rate=31878260.87/min [12230000], rate=31904347.83/min [12240000], rate=31930434.78/min [12250000], rate=31956521.74/min [12260000], rate=31982608.70/min [12270000], rate=32008695.65/min [12280000], rate=32034782.61/min [12290000], rate=32060869.57/min [12300000], rate=32086956.52/min [12310000], rate=32113043.48/min [12320000], rate=32139130.43/min [12330000], rate=32165217.39/min [12340000], rate=32191304.35/min [12350000], rate=32217391.30/min [12360000], rate=32243478.26/min [12370000], rate=32269565.22/min [12380000], rate=32295652.17/min [12390000], rate=32321739.13/min [12400000], rate=32347826.09/min [12410000], rate=32373913.04/min [12420000], rate=32400000.00/min [12430000], rate=32426086.96/min [12440000], rate=31100000.00/min [12450000], rate=31125000.00/min [12460000], rate=31150000.00/min [12470000], rate=31175000.00/min [12480000], rate=31200000.00/min [12490000], rate=31225000.00/min [12500000], rate=31250000.00/min [12510000], rate=31275000.00/min [12520000], rate=31300000.00/min [12530000], rate=31325000.00/min [12540000], rate=31350000.00/min [12550000], rate=31375000.00/min [12560000], rate=31400000.00/min [12570000], rate=31425000.00/min [12580000], rate=31450000.00/min [12590000], rate=31475000.00/min [12600000], rate=31500000.00/min [12610000], rate=31525000.00/min [12620000], rate=31550000.00/min [12630000], rate=31575000.00/min [12640000], rate=31600000.00/min [12650000], rate=31625000.00/min [12660000], rate=31650000.00/min [12670000], rate=31675000.00/min [12680000], rate=31700000.00/min [12690000], rate=31725000.00/min [12700000], rate=31750000.00/min [12710000], rate=31775000.00/min [12720000], rate=31800000.00/min [12730000], rate=31825000.00/min [12740000], rate=31850000.00/min [12750000], rate=31875000.00/min [12760000], rate=31900000.00/min [12770000], rate=31925000.00/min [12780000], rate=31950000.00/min [12790000], rate=31975000.00/min [12800000], rate=32000000.00/min [12810000], rate=32025000.00/min [12820000], rate=32050000.00/min [12830000], rate=32075000.00/min [12840000], rate=32100000.00/min [12850000], rate=32125000.00/min [12860000], rate=32150000.00/min [12870000], rate=32175000.00/min [12880000], rate=32200000.00/min [12890000], rate=32225000.00/min [12900000], rate=32250000.00/min [12910000], rate=32275000.00/min [12920000], rate=32300000.00/min [12930000], rate=32325000.00/min [12940000], rate=32350000.00/min [12950000], rate=32375000.00/min [12960000], rate=32400000.00/min [12970000], rate=32425000.00/min [12980000], rate=32450000.00/min [12990000], rate=32475000.00/min [13000000], rate=32500000.00/min [13010000], rate=31224000.00/min [13020000], rate=31248000.00/min [13030000], rate=31272000.00/min [13040000], rate=31296000.00/min [13050000], rate=31320000.00/min [13060000], rate=31344000.00/min [13070000], rate=31368000.00/min [13080000], rate=31392000.00/min [13090000], rate=31416000.00/min [13100000], rate=31440000.00/min [13110000], rate=31464000.00/min [13120000], rate=31488000.00/min [13130000], rate=31512000.00/min [13140000], rate=31536000.00/min [13150000], rate=31560000.00/min [13160000], rate=31584000.00/min [13170000], rate=31608000.00/min [13180000], rate=31632000.00/min [13190000], rate=31656000.00/min [13200000], rate=31680000.00/min [13210000], rate=31704000.00/min [13220000], rate=31728000.00/min [13230000], rate=31752000.00/min [13240000], rate=31776000.00/min [13250000], rate=31800000.00/min [13260000], rate=31824000.00/min [13270000], rate=31848000.00/min [13280000], rate=31872000.00/min [13290000], rate=31896000.00/min [13300000], rate=31920000.00/min [13310000], rate=31944000.00/min [13320000], rate=31968000.00/min [13330000], rate=31992000.00/min [13340000], rate=32016000.00/min [13350000], rate=32040000.00/min [13360000], rate=32064000.00/min [13370000], rate=32088000.00/min [13380000], rate=32112000.00/min [13390000], rate=32136000.00/min [13400000], rate=32160000.00/min [13410000], rate=32184000.00/min [13420000], rate=32208000.00/min [13430000], rate=32232000.00/min [13440000], rate=32256000.00/min [13450000], rate=32280000.00/min [13460000], rate=32304000.00/min [13470000], rate=32328000.00/min [13480000], rate=32352000.00/min [13490000], rate=32376000.00/min [13500000], rate=32400000.00/min 08:58:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_Q7O_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_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 5754 cancer introns 08:58:36 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim 08:58:36 : INFO : Running: touch /tmp/nxf.o59FiljAt1/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok 08:58:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 08:58:36 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 08:58:36 : INFO : Running: touch /tmp/nxf.o59FiljAt1/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok 08:58:36 : INFO : -found 1947 cancer introns 08:58:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 08:58:36 : INFO : Creating the BED File. 08:58:39 : INFO : Saving Bed File as 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 08:58:39 : INFO : Execution Time = 0.04 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 08:58:39 : INFO : Running: touch /tmp/nxf.o59FiljAt1/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok 08:58:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1 [W::hts_idx_load3] The index file is older than the data file: 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai 09:09:56 : INFO : Execution Time = 11.28 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1 09:09:56 : INFO : Running: touch /tmp/nxf.o59FiljAt1/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok 09:09:56 : INFO : Running: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 09:09:56 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 09:09:56 : INFO : Running: touch /tmp/nxf.o59FiljAt1/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok 09:09:56 : INFO : Running: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam [bam_sort_core] merging from 91 files and 1 in-memory blocks... 09:23:56 : INFO : Execution Time = 13.99 minutes. CMD: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam 09:23:56 : INFO : Running: touch /tmp/nxf.o59FiljAt1/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_gene_reads.ok 09:23:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 09:28:03 : INFO : Execution Time = 4.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 09:28:03 : INFO : Running: touch /tmp/nxf.o59FiljAt1/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:28:03 : INFO : Running: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 09:28:33 : INFO : Execution Time = 0.50 minutes. CMD: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp 09:28:33 : INFO : Running: touch /tmp/nxf.o59FiljAt1/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:28:33 : INFO : Running: samtools index 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 09:28:36 : INFO : Execution Time = 0.05 minutes. CMD: samtools index 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 09:28:36 : INFO : Running: touch /tmp/nxf.o59FiljAt1/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:28:36 : INFO : Running: samtools index 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 09:28:37 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 09:28:37 : INFO : Running: touch /tmp/nxf.o59FiljAt1/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:28:37 : INFO : Running: create_report 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1' 09:32:04 : INFO : Execution Time = 3.46 minutes. CMD: create_report 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1' 09:32:04 : INFO : Running: touch /tmp/nxf.o59FiljAt1/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/igv_create_html.ok 09:32:04 : INFO : done.