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[8540000], rate=18300000.00/min [8550000], rate=18321428.57/min [8560000], rate=18342857.14/min [8570000], rate=18364285.71/min [8580000], rate=18385714.29/min [8590000], rate=18407142.86/min [8600000], rate=18428571.43/min [8610000], rate=18450000.00/min [8620000], rate=18471428.57/min [8630000], rate=18492857.14/min [8640000], rate=18514285.71/min [8650000], rate=18535714.29/min [8660000], rate=18557142.86/min [8670000], rate=18578571.43/min [8680000], rate=18600000.00/min [8690000], rate=18621428.57/min [8700000], rate=18642857.14/min [8710000], rate=18664285.71/min [8720000], rate=18685714.29/min [8730000], rate=18062068.97/min [8740000], rate=18082758.62/min [8750000], rate=18103448.28/min [8760000], rate=18124137.93/min [8770000], rate=18144827.59/min [8780000], rate=18165517.24/min [8790000], rate=18186206.90/min [8800000], rate=18206896.55/min [8810000], rate=18227586.21/min [8820000], rate=18248275.86/min [8830000], rate=18268965.52/min [8840000], rate=18289655.17/min [8850000], rate=18310344.83/min [8860000], rate=18331034.48/min [8870000], rate=18351724.14/min [8880000], rate=18372413.79/min [8890000], rate=18393103.45/min [8900000], rate=18413793.10/min [8910000], rate=18434482.76/min [8920000], rate=18455172.41/min [8930000], rate=18475862.07/min [8940000], rate=18496551.72/min [8950000], rate=18517241.38/min [8960000], rate=18537931.03/min [8970000], rate=18558620.69/min [8980000], rate=18579310.34/min [8990000], rate=18600000.00/min [9000000], rate=18620689.66/min [9010000], rate=18641379.31/min [9020000], rate=18662068.97/min [9030000], rate=18682758.62/min [9040000], rate=18703448.28/min [9050000], rate=18100000.00/min [9060000], rate=18120000.00/min [9070000], rate=18140000.00/min [9080000], rate=18160000.00/min [9090000], rate=18180000.00/min [9100000], rate=18200000.00/min [9110000], rate=18220000.00/min [9120000], rate=18240000.00/min [9130000], rate=18260000.00/min [9140000], rate=18280000.00/min [9150000], rate=18300000.00/min [9160000], rate=18320000.00/min [9170000], rate=18340000.00/min [9180000], rate=18360000.00/min [9190000], rate=18380000.00/min [9200000], rate=18400000.00/min [9210000], rate=18420000.00/min [9220000], rate=18440000.00/min [9230000], rate=18460000.00/min [9240000], rate=18480000.00/min [9250000], rate=18500000.00/min [9260000], rate=18520000.00/min [9270000], rate=18540000.00/min [9280000], rate=18560000.00/min [9290000], rate=18580000.00/min [9300000], rate=18600000.00/min [9310000], rate=18620000.00/min [9320000], rate=18640000.00/min [9330000], rate=18660000.00/min [9340000], rate=18680000.00/min [9350000], rate=18700000.00/min [9360000], rate=18720000.00/min [9370000], rate=18135483.87/min [9380000], rate=18154838.71/min [9390000], rate=18174193.55/min [9400000], rate=18193548.39/min [9410000], rate=18212903.23/min [9420000], rate=18232258.06/min [9430000], rate=18251612.90/min [9440000], rate=18270967.74/min [9450000], rate=18290322.58/min [9460000], rate=18309677.42/min [9470000], rate=18329032.26/min [9480000], rate=18348387.10/min [9490000], rate=18367741.94/min [9500000], rate=18387096.77/min [9510000], rate=18406451.61/min [9520000], rate=18425806.45/min [9530000], rate=18445161.29/min [9540000], rate=18464516.13/min 09:12:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1.introns: identified 5705 cancer introns 09:12:22 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns.prelim 09:12:22 : INFO : Running: touch /tmp/nxf.pfL0Lbwqji/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 09:12:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns 09:12:22 : 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-3abdf4-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns 09:12:22 : INFO : Running: touch /tmp/nxf.pfL0Lbwqji/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 09:12:22 : INFO : -found 2598 cancer introns 09:12:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:12:23 : INFO : Creating the BED File. 09:12:28 : INFO : Saving Bed File as aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:12:29 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:12:29 : INFO : Running: touch /tmp/nxf.pfL0Lbwqji/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 09:12:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3abdf4-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 09:30:44 : INFO : Execution Time = 18.26 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3abdf4-R1_A23YTGFLT4_1 09:30:44 : INFO : Running: touch /tmp/nxf.pfL0Lbwqji/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 09:30:44 : INFO : Running: samtools sort -o aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:30:45 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:30:45 : INFO : Running: touch /tmp/nxf.pfL0Lbwqji/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 09:30:45 : INFO : Running: samtools sort -o aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 85 files and 1 in-memory blocks... 09:51:10 : INFO : Execution Time = 20.43 minutes. CMD: samtools sort -o aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.bam 09:51:10 : INFO : Running: touch /tmp/nxf.pfL0Lbwqji/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok 09:51:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.bam 09:57:19 : INFO : Execution Time = 6.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.bam 09:57:19 : INFO : Running: touch /tmp/nxf.pfL0Lbwqji/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:57:19 : INFO : Running: samtools sort -o aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 09:58:18 : INFO : Execution Time = 0.98 minutes. CMD: samtools sort -o aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp 09:58:18 : INFO : Running: touch /tmp/nxf.pfL0Lbwqji/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:58:18 : INFO : Running: samtools index aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 09:58:24 : INFO : Execution Time = 0.11 minutes. CMD: samtools index aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 09:58:24 : INFO : Running: touch /tmp/nxf.pfL0Lbwqji/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:58:24 : INFO : Running: samtools index aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 09:58:24 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 09:58:24 : INFO : Running: touch /tmp/nxf.pfL0Lbwqji/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:58:24 : INFO : Running: create_report aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1' 10:04:41 : INFO : Execution Time = 6.28 minutes. CMD: create_report aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1' 10:04:41 : INFO : Running: touch /tmp/nxf.pfL0Lbwqji/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok 10:04:41 : INFO : done.