-ctat genome lib [/tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.Hq3ReUwCSx/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary
-sample contains 14388080 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir -J /tmp/nxf.Hq3ReUwCSx/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.Hq3ReUwCSx/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
[10000], rate=27272.73/min
[20000], rate=28571.43/min
[30000], rate=29508.20/min
[40000], rate=31578.95/min
[50000], rate=33707.87/min
[60000], rate=31858.41/min
[70000], rate=28767.12/min
[80000], rate=27272.73/min
[90000], rate=28125.00/min
[100000], rate=29268.29/min
[110000], rate=29864.25/min
[120000], rate=30508.47/min
[130000], rate=31200.00/min
[140000], rate=30215.83/min
[150000], rate=29605.26/min
[160000], rate=28915.66/min
[170000], rate=28491.62/min
[180000], rate=28421.05/min
[190000], rate=28860.76/min
[200000], rate=29197.08/min
[210000], rate=29857.82/min
[220000], rate=30414.75/min
[230000], rate=30666.67/min
[240000], rate=29937.63/min
[250000], rate=29644.27/min
[260000], rate=29489.60/min
[270000], rate=29562.04/min
[280000], rate=29681.98/min
[290000], rate=30051.81/min
[300000], rate=30456.85/min
[310000], rate=31103.68/min
[320000], rate=31270.36/min
[330000], rate=31279.62/min
[340000], rate=31578.95/min
[350000], rate=31914.89/min
[360000], rate=32383.81/min
[370000], rate=32888.89/min
[380000], rate=33236.15/min
[390000], rate=33238.64/min
[400000], rate=33287.10/min
[410000], rate=33378.56/min
[420000], rate=33510.64/min
[430000], rate=33637.55/min
[440000], rate=34196.89/min
[450000], rate=34659.82/min
[460000], rate=35114.50/min
[470000], rate=35250.00/min
[480000], rate=35380.84/min
[490000], rate=35464.41/min
[500000], rate=35671.82/min
[510000], rate=35915.49/min
[520000], rate=36194.90/min
[530000], rate=36467.89/min -building interval tree based on /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=50000.00/min
[20000], rate=26086.96/min
[30000], rate=20689.66/min
[40000], rate=20000.00/min
[50000], rate=20000.00/min
[60000], rate=21301.78/min
[70000], rate=22702.70/min
[80000], rate=24242.42/min
[90000], rate=25837.32/min
[100000], rate=26905.83/min
[110000], rate=27966.10/min
[120000], rate=29032.26/min
[130000], rate=28996.28/min
[140000], rate=29065.74/min
[150000], rate=29411.76/min
[160000], rate=30094.04/min
[170000], rate=31003.04/min
[180000], rate=32432.43/min
[190000], rate=33628.32/min
[200000], rate=34188.03/min
[210000], rate=33510.64/min
[220000], rate=33673.47/min
[230000], rate=34500.00/min
[240000], rate=35207.82/min
[250000], rate=34562.21/min
[260000], rate=34210.53/min
[270000], rate=34033.61/min
[280000], rate=34355.83/min
[290000], rate=34661.35/min
[300000], rate=34749.03/min
[310000], rate=35028.25/min
[320000], rate=35555.56/min
[330000], rate=35106.38/min
[340000], rate=34931.51/min
[350000], rate=35000.00/min
[360000], rate=34726.69/min
[370000], rate=34579.44/min
[380000], rate=34756.10/min
[390000], rate=34977.58/min
[400000], rate=35294.12/min
[410000], rate=35807.86/min
[420000], rate=36206.90/min
[430000], rate=36492.22/min
[440000], rate=36871.51/min
[450000], rate=36048.06/min
[460000], rate=35612.90/min
[470000], rate=35382.69/min
[480000], rate=35164.84/min
[490000], rate=35209.58/min
[500000], rate=35128.81/min
[510000], rate=35172.41/min
[520000], rate=35414.30/min
[530000], rate=35451.51/min -building interval tree based on /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=12244.90/min
[20000], rate=13333.33/min
[30000], rate=13636.36/min
[40000], rate=14117.65/min
[50000], rate=14705.88/min
[60000], rate=16000.00/min
[70000], rate=17427.39/min
[80000], rate=18532.82/min
[90000], rate=19636.36/min
[100000], rate=21126.76/min
[110000], rate=22222.22/min
[120000], rate=23225.81/min
[130000], rate=24000.00/min
[140000], rate=24778.76/min
[150000], rate=25568.18/min
[160000], rate=26158.04/min
[170000], rate=26984.13/min
[180000], rate=27763.50/min
[190000], rate=27737.23/min
[200000], rate=27972.03/min
[210000], rate=28767.12/min
[220000], rate=29010.99/min
[230000], rate=29299.36/min
[240000], rate=29090.91/min
[250000], rate=29354.21/min
[260000], rate=29601.52/min
[270000], rate=30451.13/min
[280000], rate=30825.69/min
[290000], rate=31071.43/min
[300000], rate=31304.35/min
[310000], rate=31578.95/min
[320000], rate=32053.42/min
[330000], rate=32300.16/min
[340000], rate=32640.00/min
[350000], rate=33123.03/min
[360000], rate=33333.33/min
[370000], rate=33636.36/min
[380000], rate=33928.57/min
[390000], rate=34210.53/min
[400000], rate=34582.13/min
[410000], rate=34893.62/min
[420000], rate=35146.44/min
[430000], rate=35537.19/min
[440000], rate=34828.50/min
[450000], rate=34263.96/min
[460000], rate=33906.63/min
[470000], rate=33975.90/min
[480000], rate=34123.22/min
[490000], rate=34305.72/min
[500000], rate=34443.17/min
[510000], rate=34772.73/min
[520000], rate=35174.75/min
[530000], rate=35412.03/min -building interval tree based on /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=54545.45/min
[20000], rate=50000.00/min
[30000], rate=41860.47/min
[40000], rate=40000.00/min
[50000], rate=38961.04/min
[60000], rate=42857.14/min
[70000], rate=42857.14/min
[80000], rate=42105.26/min
[90000], rate=40601.50/min
[100000], rate=38709.68/min
[110000], rate=39285.71/min
[120000], rate=40449.44/min
[130000], rate=41711.23/min
[140000], rate=42424.24/min
[150000], rate=42452.83/min
[160000], rate=41201.72/min
[170000], rate=40963.86/min
[180000], rate=41064.64/min
[190000], rate=41304.35/min
[200000], rate=41379.31/min
[210000], rate=41311.48/min
[220000], rate=40490.80/min
[230000], rate=40588.24/min
[240000], rate=40449.44/min
[250000], rate=38961.04/min
[260000], rate=34899.33/min
[270000], rate=31952.66/min
[280000], rate=29946.52/min
[290000], rate=28384.99/min
[300000], rate=27480.92/min
[310000], rate=27393.23/min
[320000], rate=27311.52/min
[330000], rate=27423.82/min
[340000], rate=27530.36/min
[350000], rate=27777.78/min
[360000], rate=28125.00/min
[370000], rate=28461.54/min
[380000], rate=28860.76/min
[390000], rate=29177.06/min
[400000], rate=29411.76/min
[410000], rate=29638.55/min
[420000], rate=29893.24/min
[430000], rate=30246.19/min
[440000], rate=30626.45/min
[450000], rate=30963.30/min
[460000], rate=30976.43/min
[470000], rate=30921.05/min
[480000], rate=31135.14/min
[490000], rate=31276.60/min
[500000], rate=31347.96/min
[510000], rate=31644.26/min
[520000], rate=32000.00/min
[530000], rate=32317.07/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir --filt_file /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
0.00 reads per min processed...
12000000.00 reads per min processed...
6000000.00 reads per min processed...
4800000.00 reads per min processed...
4285714.29 reads per min processed...
4000000.00 reads per min processed...
3818181.82 reads per min processed...
3692307.69 reads per min processed...
3600000.00 reads per min processed...
3529411.76 reads per min processed...
3666666.67 reads per min processed...
3789473.68 reads per min processed...
3900000.00 reads per min processed...
3818181.82 reads per min processed...
3750000.00 reads per min processed...
3692307.69 reads per min processed...
3642857.14 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.Hq3ReUwCSx/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Chimeric.out.junction --tmpdir /tmp --min_junction_reads 0 --min_sum_frags 1 --require_LDAS 0 --max_promiscuity 10 --min_pct_dom_promiscuity 20 --min_novel_junction_support 1 --min_alt_pct_junction 10 --aggregate_novel_junction_dist 5 --min_spanning_frags_only 1 --genome_lib_dir /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -50948.251535
EM: Round [1] log likelihood: -50886.468358
EM: Round [2] log likelihood: -50858.458261
EM: Round [3] log likelihood: -50843.958812
EM: Round [4] log likelihood: -50836.119044
EM: Round [5] log likelihood: -50831.785574
EM: Round [6] log likelihood: -50829.331436
EM: Round [7] log likelihood: -50827.895709
EM: Round [8] log likelihood: -50827.022607
EM: Round [9] log likelihood: -50826.469514
EM: Round [10] log likelihood: -50826.105039
EM: Round [11] log likelihood: -50825.856089
EM: Round [12] log likelihood: -50825.680642
EM: Round [13] log likelihood: -50825.553651
EM: Round [14] log likelihood: -50825.459641
EM: Round [15] log likelihood: -50825.388707
EM: Round [16] log likelihood: -50825.334306
EM: Round [17] log likelihood: -50825.291988
EM: Round [18] log likelihood: -50825.258651
EM: Round [19] log likelihood: -50825.232091
EM: Round [20] log likelihood: -50825.210706
EM: Round [21] log likelihood: -50825.193320
EM: Round [22] log likelihood: -50825.179055
EM: Round [23] log likelihood: -50825.167251
EM: Round [24] log likelihood: -50825.157402
EM: Round [25] log likelihood: -50825.149119
EM: Round [26] log likelihood: -50825.142104
EM: Round [27] log likelihood: -50825.136118
EM: Round [28] log likelihood: -50825.130978
EM: Round [29] log likelihood: -50825.126536
EM: Round [30] log likelihood: -50825.122674
EM: Round [31] log likelihood: -50825.119298
EM: Round [32] log likelihood: -50825.116331
EM: Round [33] log likelihood: -50825.113710
EM: Round [34] log likelihood: -50825.111385
EM: Round [35] log likelihood: -50825.109312
EM: Round [36] log likelihood: -50825.107458
EM: Round [37] log likelihood: -50825.105793
EM: Round [38] log likelihood: -50825.104292
EM: Round [39] log likelihood: -50825.102935
EM: Round [40] log likelihood: -50825.101704
EM: Round [41] log likelihood: -50825.100585
EM: Round [42] log likelihood: -50825.099564
EM: Round [43] log likelihood: -50825.098631
EM: Round [44] log likelihood: -50825.097776
EM: Round [45] log likelihood: -50825.096990
EM: Round [46] log likelihood: -50825.096268
EM: Round [47] log likelihood: -50825.095602
EM: Round [48] log likelihood: -50825.094987
EM: Round [49] log likelihood: -50825.094418
EM: Round [50] log likelihood: -50825.093891
EM: Round [51] log likelihood: -50825.093402
EM: Round [52] log likelihood: -50825.092947
EM: Round [53] log likelihood: -50825.092524
EM: Round [54] log likelihood: -50825.092130
EM: Round [55] log likelihood: -50825.091763
EM: Round [56] log likelihood: -50825.091419
EM: Round [57] log likelihood: -50825.091098
EM: Round [58] log likelihood: -50825.090798
EM: Round [59] log likelihood: -50825.090517
EM: Round [60] log likelihood: -50825.090253
EM: Round [61] log likelihood: -50825.090006
EM: Round [62] log likelihood: -50825.089773
EM: Round [63] log likelihood: -50825.089554
EM: Round [64] log likelihood: -50825.089349
EM: Round [65] log likelihood: -50825.089155
EM: Round [66] log likelihood: -50825.088972
EM: Round [67] log likelihood: -50825.088800
EM: Round [68] log likelihood: -50825.088638
EM: Round [69] log likelihood: -50825.088484
EM: Round [70] log likelihood: -50825.088340
EM: Round [71] log likelihood: -50825.088203
EM: Round [72] log likelihood: -50825.088073
EM: Round [73] log likelihood: -50825.087950
EM: Round [74] log likelihood: -50825.087834
EM: Round [75] log likelihood: -50825.087724
EM: Round [76] log likelihood: -50825.087620
EM: Round [77] log likelihood: -50825.087521
EM: Stopping iterations at round 77 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -50935.299886
EM: Round [1] log likelihood: -50879.488145
EM: Round [2] log likelihood: -50854.349368
EM: Round [3] log likelihood: -50841.488179
EM: Round [4] log likelihood: -50834.614670
EM: Round [5] log likelihood: -50830.847822
EM: Round [6] log likelihood: -50828.726181
EM: Round [7] log likelihood: -50827.489224
EM: Round [8] log likelihood: -50826.738854
EM: Round [9] log likelihood: -50826.264517
EM: Round [10] log likelihood: -50825.952571
EM: Round [11] log likelihood: -50825.739913
EM: Round [12] log likelihood: -50825.590308
EM: Round [13] log likelihood: -50825.482195
EM: Round [14] log likelihood: -50825.402268
EM: Round [15] log likelihood: -50825.342028
EM: Round [16] log likelihood: -50825.295870
EM: Round [17] log likelihood: -50825.259992
EM: Round [18] log likelihood: -50825.231747
EM: Round [19] log likelihood: -50825.209257
EM: Round [20] log likelihood: -50825.191160
EM: Round [21] log likelihood: -50825.176456
EM: Round [22] log likelihood: -50825.164401
EM: Round [23] log likelihood: -50825.154432
EM: Round [24] log likelihood: -50825.146122
EM: Round [25] log likelihood: -50825.139141
EM: Round [26] log likelihood: -50825.133233
EM: Round [27] log likelihood: -50825.128199
EM: Round [28] log likelihood: -50825.123881
EM: Round [29] log likelihood: -50825.120153
EM: Round [30] log likelihood: -50825.116917
EM: Round [31] log likelihood: -50825.114091
EM: Round [32] log likelihood: -50825.111610
EM: Round [33] log likelihood: -50825.109421
EM: Round [34] log likelihood: -50825.107480
EM: Round [35] log likelihood: -50825.105752
EM: Round [36] log likelihood: -50825.104208
EM: Round [37] log likelihood: -50825.102821
EM: Round [38] log likelihood: -50825.101571
EM: Round [39] log likelihood: -50825.100442
EM: Round [40] log likelihood: -50825.099417
EM: Round [41] log likelihood: -50825.098485
EM: Round [42] log likelihood: -50825.097635
EM: Round [43] log likelihood: -50825.096857
EM: Round [44] log likelihood: -50825.096143
EM: Round [45] log likelihood: -50825.095487
EM: Round [46] log likelihood: -50825.094883
EM: Round [47] log likelihood: -50825.094325
EM: Round [48] log likelihood: -50825.093810
EM: Round [49] log likelihood: -50825.093331
EM: Round [50] log likelihood: -50825.092888
EM: Round [51] log likelihood: -50825.092475
EM: Round [52] log likelihood: -50825.092091
EM: Round [53] log likelihood: -50825.091733
EM: Round [54] log likelihood: -50825.091398
EM: Round [55] log likelihood: -50825.091085
EM: Round [56] log likelihood: -50825.090792
EM: Round [57] log likelihood: -50825.090517
EM: Round [58] log likelihood: -50825.090260
EM: Round [59] log likelihood: -50825.090018
EM: Round [60] log likelihood: -50825.089790
EM: Round [61] log likelihood: -50825.089576
EM: Round [62] log likelihood: -50825.089374
EM: Round [63] log likelihood: -50825.089184
EM: Round [64] log likelihood: -50825.089005
EM: Round [65] log likelihood: -50825.088835
EM: Round [66] log likelihood: -50825.088675
EM: Round [67] log likelihood: -50825.088524
EM: Round [68] log likelihood: -50825.088380
EM: Round [69] log likelihood: -50825.088245
EM: Round [70] log likelihood: -50825.088116
EM: Round [71] log likelihood: -50825.087994
EM: Round [72] log likelihood: -50825.087879
EM: Round [73] log likelihood: -50825.087769
EM: Round [74] log likelihood: -50825.087665
EM: Round [75] log likelihood: -50825.087566
EM: Stopping iterations at round 75 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter
CMD: /usr/local/src/STAR-Fusion/util/column_exclusions.pl /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered
* Running CMD: /usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 14388080 > /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM
* Running CMD: /usr/local/src/STAR-Fusion/util/append_breakpoint_junction_info.pl /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir > /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir --annotate /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot
* Running CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir
-done, see /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_likely_RT_artifacts.pl --fusions /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 406, filtered: 4073)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.Hq3ReUwCSx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass.minFFPM.0.00001.pass star-fusion.fusion_predictions.tsv
* Running CMD: /usr/local/src/STAR-Fusion/util/column_exclusions.pl star-fusion.fusion_predictions.tsv JunctionReads,SpanningFrags > star-fusion.fusion_predictions.abridged.tsv
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions star-fusion.fusion_predictions.abridged.tsv --genome_lib_dir /tmp/nxf.Hq3ReUwCSx/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000229739.4]
WARNING, no entry stored in dbm for [ENSG00000203930.12]
WARNING, no entry stored in dbm for [ENSG00000256642.1]
WARNING, no entry stored in dbm for [ENSG00000278733.1]
WARNING, no entry stored in dbm for [ENSG00000234715.2]
WARNING, no entry stored in dbm for [ENSG00000251314.2]
WARNING, no entry stored in dbm for [ENSG00000259343.7]
WARNING, no entry stored in dbm for [ENSG00000133519.12]
WARNING, no entry stored in dbm for [ENSG00000215478.8]
WARNING, no entry stored in dbm for [ENSG00000206585.1]
WARNING, no entry stored in dbm for [ENSG00000278099.1]
WARNING, no entry stored in dbm for [ENSG00000273768.1]
WARNING, no entry stored in dbm for [ENSG00000277918.1]
WARNING, no entry stored in dbm for [ENSG00000206737.1]
WARNING, no entry stored in dbm for [ENSG00000207389.1]
WARNING, no entry stored in dbm for [ENSG00000207513.1]
WARNING, no entry stored in dbm for [ENSG00000206588.1]
WARNING, no entry stored in dbm for [ENSG00000206596.1]
WARNING, no entry stored in dbm for [ENSG00000207005.1]
WARNING, no entry stored in dbm for [ENSG00000206652.1]
WARNING, no entry stored in dbm for [ENSG00000279217.1]
WARNING, no entry stored in dbm for [ENSG00000279217.1]
WARNING, no entry stored in dbm for [ENSG00000284731.1]
WARNING, no entry stored in dbm for [ENSG00000261659.2]
WARNING, no entry stored in dbm for [ENSG00000281732.1]
WARNING, no entry stored in dbm for [ENSG00000241933.1]
WARNING, no entry stored in dbm for [ENSG00000228889.7]
WARNING, no entry stored in dbm for [ENSG00000245156.1]
WARNING, no entry stored in dbm for [ENSG00000266179.2]
WARNING, no entry stored in dbm for [ENSG00000108448.22]
WARNING, no entry stored in dbm for [ENSG00000180279.7]
WARNING, no entry stored in dbm for [ENSG00000237401.8]
WARNING, no entry stored in dbm for [ENSG00000205853.12]
WARNING, no entry stored in dbm for [ENSG00000249031.1]
WARNING, no entry stored in dbm for [ENSG00000277072.5]
WARNING, no entry stored in dbm for [ENSG00000253600.1]
WARNING, no entry stored in dbm for [ENSG00000283627.1]
WARNING, no entry stored in dbm for [ENSG00000254088.1]
WARNING, no entry stored in dbm for [ENSG00000234771.3]
WARNING, no entry stored in dbm for [ENSG00000227906.8]
WARNING, no entry stored in dbm for [ENSG00000228463.10]
WARNING, no entry stored in dbm for [ENSG00000226356.2]
WARNING, no entry stored in dbm for [ENSG00000239437.3]
WARNING, no entry stored in dbm for [ENSG00000266420.2]
WARNING, no entry stored in dbm for [ENSG00000239899.3]
WARNING, no entry stored in dbm for [ENSG00000241175.3]
WARNING, no entry stored in dbm for [ENSG00000244642.3]
WARNING, no entry stored in dbm for [ENSG00000201428.1]
WARNING, no entry stored in dbm for [ENSG00000199683.1]
WARNING, no entry stored in dbm for [ENSG00000237000.1]
WARNING, no entry stored in dbm for [ENSG00000227195.11]
WARNING, no entry stored in dbm for [ENSG00000230082.1]
WARNING, no entry stored in dbm for [ENSG00000180385.8]
WARNING, no entry stored in dbm for [ENSG00000244257.5]
WARNING, no entry stored in dbm for [ENSG00000239888.3]
WARNING, no entry stored in dbm for [ENSG00000281344.1]
WARNING, no entry stored in dbm for [ENSG00000279217.1]
WARNING, no entry stored in dbm for [ENSG00000225342.2]
WARNING, no entry stored in dbm for [ENSG00000229739.4]
WARNING, no entry stored in dbm for [ENSG00000288538.1]
WARNING, no entry stored in dbm for [ENSG00000233590.1]
WARNING, no entry stored in dbm for [ENSG00000286999.1]
WARNING, no entry stored in dbm for [ENSG00000255875.2]
WARNING, no entry stored in dbm for [ENSG00000232706.3]
WARNING, no entry stored in dbm for [ENSG00000181577.16]
WARNING, no entry stored in dbm for [ENSG00000283183.2]
WARNING, no entry stored in dbm for [ENSG00000245532.9]
WARNING, no entry stored in dbm for [ENSG00000249476.2]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000283426.1]
WARNING, no entry stored in dbm for [ENSG00000230130.1]
WARNING, no entry stored in dbm for [ENSG00000198763.3]
WARNING, no entry stored in dbm for [ENSG00000288107.1]
WARNING, no entry stored in dbm for [ENSG00000258725.2]
WARNING, no entry stored in dbm for [ENSG00000270960.1]
WARNING, no entry stored in dbm for [ENSG00000275212.3]
WARNING, no entry stored in dbm for [ENSG00000267779.7]
WARNING, no entry stored in dbm for [ENSG00000253819.2]
WARNING, no entry stored in dbm for [ENSG00000225108.1]
WARNING, no entry stored in dbm for [ENSG00000278811.4]
WARNING, no entry stored in dbm for [ENSG00000203441.2]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000260807.7]
WARNING, no entry stored in dbm for [ENSG00000131885.17]
WARNING, no entry stored in dbm for [ENSG00000253716.6]
WARNING, no entry stored in dbm for [ENSG00000261471.1]
WARNING, no entry stored in dbm for [ENSG00000229992.1]
WARNING, no entry stored in dbm for [ENSG00000206337.12]
WARNING, no entry stored in dbm for [ENSG00000231721.7]
WARNING, no entry stored in dbm for [ENSG00000255471.1]
WARNING, no entry stored in dbm for [ENSG00000231375.1]
WARNING, no entry stored in dbm for [ENSG00000241684.6]
WARNING, no entry stored in dbm for [ENSG00000263883.1]
WARNING, no entry stored in dbm for [ENSG00000283103.3]
WARNING, no entry stored in dbm for [ENSG00000197085.11]
WARNING, no entry stored in dbm for [ENSG00000231700.3]
WARNING, no entry stored in dbm for [ENSG00000227068.1]
WARNING, no entry stored in dbm for [ENSG00000230630.5]
WARNING, no entry stored in dbm for [ENSG00000226989.1]
WARNING, no entry stored in dbm for [ENSG00000244642.3]
WARNING, no entry stored in dbm for [ENSG00000278969.1]
WARNING, no entry stored in dbm for [ENSG00000172460.17]
WARNING, no entry stored in dbm for [ENSG00000270190.1]
WARNING, no entry stored in dbm for [ENSG00000249072.1]
WARNING, no entry stored in dbm for [ENSG00000271699.5]
WARNING, no entry stored in dbm for [ENSG00000260672.1]
WARNING, no entry stored in dbm for [ENSG00000244198.7]
WARNING, no entry stored in dbm for [ENSG00000251143.1]
WARNING, no entry stored in dbm for [ENSG00000258779.8]
WARNING, no entry stored in dbm for [ENSG00000275285.1]
WARNING, no entry stored in dbm for [ENSG00000246203.2]
WARNING, no entry stored in dbm for [ENSG00000226668.5]
WARNING, no entry stored in dbm for [ENSG00000213613.2]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000184991.3]
WARNING, no entry stored in dbm for [ENSG00000233955.1]
WARNING, no entry stored in dbm for [ENSG00000225871.2]
WARNING, no entry stored in dbm for [ENSG00000264635.1]
WARNING, no entry stored in dbm for [ENSG00000282924.1]
WARNING, no entry stored in dbm for [ENSG00000280287.1]
WARNING, no entry stored in dbm for [ENSG00000265533.1]
WARNING, no entry stored in dbm for [ENSG00000267053.8]
WARNING, no entry stored in dbm for [ENSG00000228998.4]
WARNING, no entry stored in dbm for [ENSG00000254102.2]
WARNING, no entry stored in dbm for [ENSG00000279581.1]
WARNING, no entry stored in dbm for [ENSG00000223628.2]
WARNING, no entry stored in dbm for [ENSG00000231414.1]
WARNING, no entry stored in dbm for [ENSG00000279077.1]
WARNING, no entry stored in dbm for [ENSG00000280161.1]
WARNING, no entry stored in dbm for [ENSG00000285106.2]
WARNING, no entry stored in dbm for [ENSG00000268189.2]
WARNING, no entry stored in dbm for [ENSG00000264578.1]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
* STAR-Fusion complete. See output: /tmp/nxf.Hq3ReUwCSx/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)