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[7990000], rate=9783673.47/min [8000000], rate=9795918.37/min [8010000], rate=9612000.00/min [8020000], rate=9624000.00/min [8030000], rate=9636000.00/min [8040000], rate=9648000.00/min [8050000], rate=9660000.00/min [8060000], rate=9672000.00/min [8070000], rate=9684000.00/min [8080000], rate=9696000.00/min [8090000], rate=9708000.00/min [8100000], rate=9720000.00/min [8110000], rate=9732000.00/min [8120000], rate=9744000.00/min [8130000], rate=9756000.00/min [8140000], rate=9576470.59/min [8150000], rate=9588235.29/min [8160000], rate=9600000.00/min [8170000], rate=9611764.71/min [8180000], rate=9623529.41/min [8190000], rate=9635294.12/min [8200000], rate=9647058.82/min [8210000], rate=9658823.53/min [8220000], rate=9670588.24/min [8230000], rate=9682352.94/min [8240000], rate=9694117.65/min [8250000], rate=9705882.35/min [8260000], rate=9717647.06/min [8270000], rate=9729411.76/min [8280000], rate=9741176.47/min [8290000], rate=9752941.18/min [8300000], rate=9576923.08/min [8310000], rate=9588461.54/min [8320000], rate=9600000.00/min [8330000], rate=9611538.46/min [8340000], rate=9623076.92/min [8350000], rate=9634615.38/min [8360000], rate=9646153.85/min [8370000], rate=9657692.31/min [8380000], rate=9669230.77/min [8390000], rate=9680769.23/min [8400000], rate=9692307.69/min [8410000], rate=9703846.15/min [8420000], rate=9715384.62/min [8430000], rate=9726923.08/min [8440000], rate=9738461.54/min [8450000], rate=9750000.00/min [8460000], rate=9761538.46/min [8470000], rate=9773076.92/min [8480000], rate=9784615.38/min [8490000], rate=9796153.85/min [8500000], rate=9807692.31/min [8510000], rate=9819230.77/min [8520000], rate=9830769.23/min [8530000], rate=9656603.77/min [8540000], rate=9667924.53/min [8550000], rate=9679245.28/min [8560000], rate=9690566.04/min [8570000], rate=9701886.79/min [8580000], rate=9713207.55/min [8590000], rate=9724528.30/min [8600000], rate=9735849.06/min [8610000], rate=9747169.81/min [8620000], rate=9758490.57/min [8630000], rate=9769811.32/min [8640000], rate=9781132.08/min [8650000], rate=9792452.83/min [8660000], rate=9803773.58/min [8670000], rate=9815094.34/min [8680000], rate=9826415.09/min [8690000], rate=9837735.85/min [8700000], rate=9849056.60/min [8710000], rate=9677777.78/min [8720000], rate=9688888.89/min [8730000], rate=9700000.00/min [8740000], rate=9711111.11/min [8750000], rate=9722222.22/min [8760000], rate=9733333.33/min [8770000], rate=9744444.44/min [8780000], rate=9755555.56/min [8790000], rate=9766666.67/min [8800000], rate=9777777.78/min [8810000], rate=9788888.89/min [8820000], rate=9800000.00/min [8830000], rate=9811111.11/min [8840000], rate=9822222.22/min [8850000], rate=9833333.33/min [8860000], rate=9844444.44/min [8870000], rate=9855555.56/min [8880000], rate=9687272.73/min [8890000], rate=9698181.82/min [8900000], rate=9709090.91/min [8910000], rate=9720000.00/min [8920000], rate=9730909.09/min [8930000], rate=9741818.18/min [8940000], rate=9752727.27/min [8950000], rate=9763636.36/min [8960000], rate=9774545.45/min [8970000], rate=9785454.55/min [8980000], rate=9796363.64/min [8990000], rate=9807272.73/min [9000000], rate=9818181.82/min [9010000], rate=9829090.91/min [9020000], rate=9840000.00/min [9030000], rate=9850909.09/min [9040000], rate=9685714.29/min [9050000], rate=9696428.57/min [9060000], rate=9707142.86/min [9070000], rate=9717857.14/min [9080000], rate=9728571.43/min [9090000], rate=9739285.71/min [9100000], rate=9750000.00/min [9110000], rate=9760714.29/min [9120000], rate=9771428.57/min [9130000], rate=9782142.86/min [9140000], rate=9792857.14/min [9150000], rate=9803571.43/min [9160000], rate=9814285.71/min [9170000], rate=9825000.00/min [9180000], rate=9835714.29/min [9190000], rate=9846428.57/min [9200000], rate=9684210.53/min [9210000], rate=9694736.84/min [9220000], rate=9705263.16/min [9230000], rate=9715789.47/min [9240000], rate=9726315.79/min [9250000], rate=9736842.11/min [9260000], rate=9747368.42/min [9270000], rate=9757894.74/min [9280000], rate=9768421.05/min [9290000], rate=9778947.37/min [9300000], rate=9789473.68/min [9310000], rate=9800000.00/min [9320000], rate=9810526.32/min [9330000], rate=9821052.63/min [9340000], rate=9831578.95/min [9350000], rate=9842105.26/min [9360000], rate=9682758.62/min [9370000], rate=9693103.45/min [9380000], rate=9703448.28/min [9390000], rate=9713793.10/min [9400000], rate=9724137.93/min [9410000], rate=9734482.76/min [9420000], rate=9744827.59/min [9430000], rate=9755172.41/min [9440000], rate=9765517.24/min [9450000], rate=9775862.07/min [9460000], rate=9786206.90/min [9470000], rate=9796551.72/min [9480000], rate=9806896.55/min [9490000], rate=9817241.38/min [9500000], rate=9827586.21/min [9510000], rate=9837931.03/min [9520000], rate=9848275.86/min [9530000], rate=9691525.42/min [9540000], rate=9701694.92/min [9550000], rate=9711864.41/min [9560000], rate=9722033.90/min [9570000], rate=9732203.39/min [9580000], rate=9742372.88/min [9590000], rate=9752542.37/min [9600000], rate=9762711.86/min [9610000], rate=9772881.36/min [9620000], rate=9783050.85/min [9630000], rate=9793220.34/min [9640000], rate=9803389.83/min [9650000], rate=9813559.32/min 08:52:40 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00252_23H5VFLT4_s04.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00252_23H5VFLT4_s04.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_00252_23H5VFLT4_s04.introns: identified 6947 cancer introns 08:52:41 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00252_23H5VFLT4_s04.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00252_23H5VFLT4_s04.cancer.introns.prelim 08:52:41 : INFO : Running: touch /tmp/nxf.JzZhgkpILl/tih_rna_sample_00252_23H5VFLT4_s04.chckpts/prelim_introns.ok 08:52:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00252_23H5VFLT4_s04.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00252_23H5VFLT4_s04.cancer.introns 08:52:42 : 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_00252_23H5VFLT4_s04.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00252_23H5VFLT4_s04.cancer.introns 08:52:42 : INFO : Running: touch /tmp/nxf.JzZhgkpILl/tih_rna_sample_00252_23H5VFLT4_s04.chckpts/introns_filtered.ok 08:52:42 : INFO : -found 3251 cancer introns 08:52:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00252_23H5VFLT4_s04.introns --cancer_introns tih_rna_sample_00252_23H5VFLT4_s04.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00252_23H5VFLT4_s04.introns.for_IGV.bed 08:52:42 : INFO : Creating the BED File. 08:52:53 : INFO : Saving Bed File as tih_rna_sample_00252_23H5VFLT4_s04.introns.for_IGV.bed 08:52:53 : INFO : Execution Time = 0.19 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00252_23H5VFLT4_s04.introns --cancer_introns tih_rna_sample_00252_23H5VFLT4_s04.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00252_23H5VFLT4_s04.introns.for_IGV.bed 08:52:53 : INFO : Running: touch /tmp/nxf.JzZhgkpILl/tih_rna_sample_00252_23H5VFLT4_s04.chckpts/intron_igv_bed.ok 08:52:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00252_23H5VFLT4_s04.introns.for_IGV.bed --bam tih_rna_sample_00252_23H5VFLT4_s04.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00252_23H5VFLT4_s04 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00252_23H5VFLT4_s04.Aligned.sortedByCoord.out.bam.bai 09:21:59 : INFO : Execution Time = 29.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00252_23H5VFLT4_s04.introns.for_IGV.bed --bam tih_rna_sample_00252_23H5VFLT4_s04.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00252_23H5VFLT4_s04 09:21:59 : INFO : Running: touch /tmp/nxf.JzZhgkpILl/tih_rna_sample_00252_23H5VFLT4_s04.chckpts/reads_alignments_extracted.ok 09:21:59 : INFO : Running: samtools sort -o tih_rna_sample_00252_23H5VFLT4_s04.cancer_intron_reads.sorted.bam tih_rna_sample_00252_23H5VFLT4_s04.cancer_intron_reads.bam 09:21:59 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00252_23H5VFLT4_s04.cancer_intron_reads.sorted.bam tih_rna_sample_00252_23H5VFLT4_s04.cancer_intron_reads.bam 09:21:59 : INFO : Running: touch /tmp/nxf.JzZhgkpILl/tih_rna_sample_00252_23H5VFLT4_s04.chckpts/sort_cancer_intron_reads.ok 09:22:00 : INFO : Running: samtools sort -o tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.bam tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.bam [bam_sort_core] merging from 108 files and 1 in-memory blocks... 09:49:51 : INFO : Execution Time = 27.86 minutes. CMD: samtools sort -o tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.bam tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.bam 09:49:51 : INFO : Running: touch /tmp/nxf.JzZhgkpILl/tih_rna_sample_00252_23H5VFLT4_s04.chckpts/sort_gene_reads.ok 09:49:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.bam 09:59:15 : INFO : Execution Time = 9.39 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.bam 09:59:15 : INFO : Running: touch /tmp/nxf.JzZhgkpILl/tih_rna_sample_00252_23H5VFLT4_s04.chckpts/tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.sifted.bam.tmp.ok 09:59:15 : INFO : Running: samtools sort -o tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.sifted.bam tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 9 files and 1 in-memory blocks... 10:01:40 : INFO : Execution Time = 2.42 minutes. CMD: samtools sort -o tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.sifted.bam tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.sifted.bam.tmp 10:01:40 : INFO : Running: touch /tmp/nxf.JzZhgkpILl/tih_rna_sample_00252_23H5VFLT4_s04.chckpts/tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:01:40 : INFO : Running: samtools index tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.sifted.bam 10:01:55 : INFO : Execution Time = 0.26 minutes. CMD: samtools index tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.sifted.bam 10:01:55 : INFO : Running: touch /tmp/nxf.JzZhgkpILl/tih_rna_sample_00252_23H5VFLT4_s04.chckpts/tih_rna_sample_00252_23H5VFLT4_s04.gene_reads.sorted.sifted.bam.indexed.ok 10:01:55 : INFO : Running: samtools index tih_rna_sample_00252_23H5VFLT4_s04.cancer_intron_reads.sorted.bam 10:01:56 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00252_23H5VFLT4_s04.cancer_intron_reads.sorted.bam 10:01:56 : INFO : Running: touch /tmp/nxf.JzZhgkpILl/tih_rna_sample_00252_23H5VFLT4_s04.chckpts/tih_rna_sample_00252_23H5VFLT4_s04.cancer_intron_reads.sorted.bam.indexed.ok 10:01:56 : INFO : Running: create_report tih_rna_sample_00252_23H5VFLT4_s04.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00252_23H5VFLT4_s04.ctat-splicing.igv.html --track-config tih_rna_sample_00252_23H5VFLT4_s04.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00252_23H5VFLT4_s04' 10:10:35 : INFO : Execution Time = 8.66 minutes. CMD: create_report tih_rna_sample_00252_23H5VFLT4_s04.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00252_23H5VFLT4_s04.ctat-splicing.igv.html --track-config tih_rna_sample_00252_23H5VFLT4_s04.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00252_23H5VFLT4_s04' 10:10:35 : INFO : Running: touch /tmp/nxf.JzZhgkpILl/tih_rna_sample_00252_23H5VFLT4_s04.chckpts/igv_create_html.ok 10:10:35 : INFO : done.