-ctat genome lib [/tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.7fFu7tgbmw/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary
-sample contains 14304435 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir -J /tmp/nxf.7fFu7tgbmw/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_3.Chimeric.out.junction -O /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.7fFu7tgbmw/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_3.Chimeric.out.junction
-building interval tree based on /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
[10000], rate=75000.00/min
[20000], rate=54545.45/min
[30000], rate=52941.18/min
[40000], rate=53333.33/min
[50000], rate=55555.56/min
[60000], rate=53731.34/min
[70000], rate=52500.00/min
[80000], rate=54545.45/min
[90000], rate=55102.04/min
[100000], rate=54054.05/min
[110000], rate=54098.36/min
[120000], rate=55384.62/min
[130000], rate=57352.94/min
[140000], rate=57931.03/min
[150000], rate=59210.53/min
[160000], rate=60000.00/min
[170000], rate=60000.00/min
[180000], rate=61016.95/min
[190000], rate=60317.46/min
[200000], rate=60913.71/min -building interval tree based on /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
[10000], rate=40000.00/min
[20000], rate=46153.85/min
[30000], rate=51428.57/min
[40000], rate=55813.95/min
[50000], rate=55555.56/min
[60000], rate=58064.52/min
[70000], rate=62686.57/min
[80000], rate=67605.63/min
[90000], rate=65060.24/min
[100000], rate=65934.07/min
[110000], rate=62857.14/min
[120000], rate=61016.95/min
[130000], rate=60937.50/min
[140000], rate=60869.57/min
[150000], rate=61643.84/min
[160000], rate=61935.48/min
[170000], rate=60355.03/min
[180000], rate=59340.66/min
[190000], rate=59375.00/min
[200000], rate=60301.51/min -building interval tree based on /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
[10000], rate=37500.00/min
[20000], rate=40000.00/min
[30000], rate=45000.00/min
[40000], rate=47058.82/min
[50000], rate=43478.26/min
[60000], rate=41379.31/min
[70000], rate=40776.70/min
[80000], rate=42105.26/min
[90000], rate=43902.44/min
[100000], rate=46153.85/min
[110000], rate=48175.18/min
[120000], rate=50349.65/min
[130000], rate=52348.99/min
[140000], rate=53846.15/min
[150000], rate=54878.05/min
[160000], rate=53932.58/min
[170000], rate=52307.69/min
[180000], rate=52427.18/min
[190000], rate=53271.03/min
[200000], rate=53333.33/min -building interval tree based on /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
[10000], rate=120000.00/min
[20000], rate=100000.00/min
[30000], rate=46153.85/min
[40000], rate=40677.97/min
[50000], rate=39473.68/min
[60000], rate=39560.44/min
[70000], rate=40000.00/min
[80000], rate=41025.64/min
[90000], rate=42857.14/min
[100000], rate=44776.12/min
[110000], rate=46153.85/min
[120000], rate=47368.42/min
[130000], rate=49367.09/min
[140000], rate=48554.91/min
[150000], rate=47120.42/min
[160000], rate=46601.94/min
[170000], rate=46363.64/min
[180000], rate=46351.93/min
[190000], rate=46530.61/min
[200000], rate=46875.00/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir --filt_file /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
3000000.00 reads per min processed...
2400000.00 reads per min processed...
2250000.00 reads per min processed...
2400000.00 reads per min processed...
2500000.00 reads per min processed...
2571428.57 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.7fFu7tgbmw/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_3.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.7fFu7tgbmw/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -15095.165852
EM: Round [1] log likelihood: -15085.949395
EM: Round [2] log likelihood: -15081.588263
EM: Round [3] log likelihood: -15079.198125
EM: Round [4] log likelihood: -15077.846422
EM: Round [5] log likelihood: -15077.075442
EM: Round [6] log likelihood: -15076.626803
EM: Round [7] log likelihood: -15076.356110
EM: Round [8] log likelihood: -15076.184985
EM: Round [9] log likelihood: -15076.071238
EM: Round [10] log likelihood: -15075.991872
EM: Round [11] log likelihood: -15075.934014
EM: Round [12] log likelihood: -15075.890206
EM: Round [13] log likelihood: -15075.855967
EM: Round [14] log likelihood: -15075.828501
EM: Round [15] log likelihood: -15075.805999
EM: Round [16] log likelihood: -15075.787248
EM: Round [17] log likelihood: -15075.771411
EM: Round [18] log likelihood: -15075.757889
EM: Round [19] log likelihood: -15075.746245
EM: Round [20] log likelihood: -15075.736148
EM: Round [21] log likelihood: -15075.727346
EM: Round [22] log likelihood: -15075.719639
EM: Round [23] log likelihood: -15075.712868
EM: Round [24] log likelihood: -15075.706903
EM: Round [25] log likelihood: -15075.701636
EM: Round [26] log likelihood: -15075.696977
EM: Round [27] log likelihood: -15075.692850
EM: Round [28] log likelihood: -15075.689190
EM: Round [29] log likelihood: -15075.685942
EM: Round [30] log likelihood: -15075.683056
EM: Round [31] log likelihood: -15075.680491
EM: Round [32] log likelihood: -15075.678210
EM: Round [33] log likelihood: -15075.676180
EM: Round [34] log likelihood: -15075.674373
EM: Round [35] log likelihood: -15075.672763
EM: Round [36] log likelihood: -15075.671330
EM: Round [37] log likelihood: -15075.670052
EM: Round [38] log likelihood: -15075.668914
EM: Round [39] log likelihood: -15075.667899
EM: Round [40] log likelihood: -15075.666993
EM: Round [41] log likelihood: -15075.666186
EM: Round [42] log likelihood: -15075.665465
EM: Round [43] log likelihood: -15075.664822
EM: Round [44] log likelihood: -15075.664248
EM: Round [45] log likelihood: -15075.663735
EM: Round [46] log likelihood: -15075.663277
EM: Round [47] log likelihood: -15075.662868
EM: Round [48] log likelihood: -15075.662502
EM: Round [49] log likelihood: -15075.662175
EM: Round [50] log likelihood: -15075.661883
EM: Round [51] log likelihood: -15075.661622
EM: Round [52] log likelihood: -15075.661388
EM: Round [53] log likelihood: -15075.661178
EM: Round [54] log likelihood: -15075.660991
EM: Round [55] log likelihood: -15075.660823
EM: Round [56] log likelihood: -15075.660673
EM: Round [57] log likelihood: -15075.660539
EM: Round [58] log likelihood: -15075.660418
EM: Round [59] log likelihood: -15075.660310
EM: Round [60] log likelihood: -15075.660213
EM: Stopping iterations at round 60 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -15091.459083
EM: Round [1] log likelihood: -15083.592997
EM: Round [2] log likelihood: -15080.063050
EM: Round [3] log likelihood: -15078.246122
EM: Round [4] log likelihood: -15077.265033
EM: Round [5] log likelihood: -15076.720830
EM: Round [6] log likelihood: -15076.407558
EM: Round [7] log likelihood: -15076.217459
EM: Round [8] log likelihood: -15076.094805
EM: Round [9] log likelihood: -15076.010701
EM: Round [10] log likelihood: -15075.949826
EM: Round [11] log likelihood: -15075.903746
EM: Round [12] log likelihood: -15075.867607
EM: Round [13] log likelihood: -15075.838475
EM: Round [14] log likelihood: -15075.814490
EM: Round [15] log likelihood: -15075.794422
EM: Round [16] log likelihood: -15075.777422
EM: Round [17] log likelihood: -15075.762882
EM: Round [18] log likelihood: -15075.750353
EM: Round [19] log likelihood: -15075.739494
EM: Round [20] log likelihood: -15075.730039
EM: Round [21] log likelihood: -15075.721778
EM: Round [22] log likelihood: -15075.714537
EM: Round [23] log likelihood: -15075.708178
EM: Round [24] log likelihood: -15075.702582
EM: Round [25] log likelihood: -15075.697651
EM: Round [26] log likelihood: -15075.693300
EM: Round [27] log likelihood: -15075.689458
EM: Round [28] log likelihood: -15075.686061
EM: Round [29] log likelihood: -15075.683057
EM: Round [30] log likelihood: -15075.680399
EM: Round [31] log likelihood: -15075.678045
EM: Round [32] log likelihood: -15075.675959
EM: Round [33] log likelihood: -15075.674111
EM: Round [34] log likelihood: -15075.672473
EM: Round [35] log likelihood: -15075.671020
EM: Round [36] log likelihood: -15075.669731
EM: Round [37] log likelihood: -15075.668587
EM: Round [38] log likelihood: -15075.667572
EM: Round [39] log likelihood: -15075.666670
EM: Round [40] log likelihood: -15075.665870
EM: Round [41] log likelihood: -15075.665158
EM: Round [42] log likelihood: -15075.664526
EM: Round [43] log likelihood: -15075.663964
EM: Round [44] log likelihood: -15075.663465
EM: Round [45] log likelihood: -15075.663020
EM: Round [46] log likelihood: -15075.662625
EM: Round [47] log likelihood: -15075.662273
EM: Round [48] log likelihood: -15075.661960
EM: Round [49] log likelihood: -15075.661681
EM: Round [50] log likelihood: -15075.661432
EM: Round [51] log likelihood: -15075.661211
EM: Round [52] log likelihood: -15075.661014
EM: Round [53] log likelihood: -15075.660838
EM: Round [54] log likelihood: -15075.660681
EM: Round [55] log likelihood: -15075.660541
EM: Round [56] log likelihood: -15075.660416
EM: Round [57] log likelihood: -15075.660305
EM: Round [58] log likelihood: -15075.660205
EM: Stopping iterations at round 58 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 14304435 > /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir > /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir --annotate /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir
-done, see /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 193, filtered: 1896)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000285410.1]
WARNING, no entry stored in dbm for [ENSG00000216824.2]
WARNING, no entry stored in dbm for [ENSG00000257495.5]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000248994.2]
WARNING, no entry stored in dbm for [ENSG00000250307.2]
WARNING, no entry stored in dbm for [ENSG00000256817.1]
WARNING, no entry stored in dbm for [ENSG00000234782.3]
WARNING, no entry stored in dbm for [ENSG00000224533.4]
WARNING, no entry stored in dbm for [ENSG00000215296.10]
WARNING, no entry stored in dbm for [ENSG00000240549.2]
WARNING, no entry stored in dbm for [ENSG00000287338.1]
WARNING, no entry stored in dbm for [ENSG00000128438.10]
WARNING, no entry stored in dbm for [ENSG00000248660.1]
WARNING, no entry stored in dbm for [ENSG00000206983.1]
WARNING, no entry stored in dbm for [ENSG00000242986.2]
WARNING, no entry stored in dbm for [ENSG00000230559.1]
WARNING, no entry stored in dbm for [ENSG00000286847.1]
WARNING, no entry stored in dbm for [ENSG00000257634.1]
WARNING, no entry stored in dbm for [ENSG00000270793.1]
WARNING, no entry stored in dbm for [ENSG00000253642.6]
WARNING, no entry stored in dbm for [ENSG00000260278.1]
WARNING, no entry stored in dbm for [ENSG00000223704.2]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000233237.8]
WARNING, no entry stored in dbm for [ENSG00000245067.7]
WARNING, no entry stored in dbm for [ENSG00000279620.1]
WARNING, no entry stored in dbm for [ENSG00000225465.10]
WARNING, no entry stored in dbm for [ENSG00000185684.15]
WARNING, no entry stored in dbm for [ENSG00000251562.8]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000225539.7]
WARNING, no entry stored in dbm for [ENSG00000232000.3]
WARNING, no entry stored in dbm for [ENSG00000230773.9]
WARNING, no entry stored in dbm for [ENSG00000223966.1]
WARNING, no entry stored in dbm for [ENSG00000230805.8]
WARNING, no entry stored in dbm for [ENSG00000226645.1]
WARNING, no entry stored in dbm for [ENSG00000265179.7]
WARNING, no entry stored in dbm for [ENSG00000254924.2]
WARNING, no entry stored in dbm for [ENSG00000285799.1]
WARNING, no entry stored in dbm for [ENSG00000254741.1]
WARNING, no entry stored in dbm for [ENSG00000230869.1]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000242586.1]
WARNING, no entry stored in dbm for [ENSG00000227733.10]
WARNING, no entry stored in dbm for [ENSG00000205976.4]
WARNING, no entry stored in dbm for [ENSG00000258320.1]
WARNING, no entry stored in dbm for [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000287232.1]
WARNING, no entry stored in dbm for [ENSG00000285329.1]
WARNING, no entry stored in dbm for [ENSG00000177359.20]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000275734.2]
WARNING, no entry stored in dbm for [ENSG00000262420.3]
WARNING, no entry stored in dbm for [ENSG00000228113.7]
* STAR-Fusion complete. See output: /tmp/nxf.7fFu7tgbmw/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)