-ctat genome lib [/tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.riUCU57EJJ/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary
-sample contains 116041077 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir -J /tmp/nxf.riUCU57EJJ/dna_s762.Chimeric.out.junction -O /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.riUCU57EJJ/dna_s762.Chimeric.out.junction
-building interval tree based on /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=66666.67/min
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[760000], rate=53773.58/min -building interval tree based on /tmp/nxf.riUCU57EJJ/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
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[750000], rate=53191.49/min -building interval tree based on /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes
[10000], rate=200000.00/min
[20000], rate=240000.00/min
[30000], rate=200000.00/min
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[750000], rate=48754.06/min -building interval tree based on /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes
[10000], rate=54545.45/min
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[30000], rate=62068.97/min
[40000], rate=63157.89/min
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[730000], rate=47096.77/min
[740000], rate=46984.13/min
[750000], rate=46923.88/min
[760000], rate=46913.58/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir --filt_file /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
6000000.00 reads per min processed...
4000000.00 reads per min processed...
3600000.00 reads per min processed...
4000000.00 reads per min processed...
3750000.00 reads per min processed...
3600000.00 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...
3473684.21 reads per min processed...
3600000.00 reads per min processed...
3545454.55 reads per min processed...
3652173.91 reads per min processed...
3600000.00 reads per min processed...
3555555.56 reads per min processed...
3642857.14 reads per min processed...
3600000.00 reads per min processed...
3677419.35 reads per min processed...
3636363.64 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.riUCU57EJJ/dna_s762.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.riUCU57EJJ/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -141573.485122
EM: Round [1] log likelihood: -141508.076251
EM: Round [2] log likelihood: -141485.912999
EM: Round [3] log likelihood: -141475.994953
EM: Round [4] log likelihood: -141470.829676
EM: Round [5] log likelihood: -141467.915344
EM: Round [6] log likelihood: -141466.186338
EM: Round [7] log likelihood: -141465.117727
EM: Round [8] log likelihood: -141464.432070
EM: Round [9] log likelihood: -141463.976814
EM: Round [10] log likelihood: -141463.665262
EM: Round [11] log likelihood: -141463.446459
EM: Round [12] log likelihood: -141463.289407
EM: Round [13] log likelihood: -141463.174606
EM: Round [14] log likelihood: -141463.089398
EM: Round [15] log likelihood: -141463.025327
EM: Round [16] log likelihood: -141462.976610
EM: Round [17] log likelihood: -141462.939200
EM: Round [18] log likelihood: -141462.910222
EM: Round [19] log likelihood: -141462.887596
EM: Round [20] log likelihood: -141462.869801
EM: Round [21] log likelihood: -141462.855711
EM: Round [22] log likelihood: -141462.844485
EM: Round [23] log likelihood: -141462.835489
EM: Round [24] log likelihood: -141462.828241
EM: Round [25] log likelihood: -141462.822371
EM: Round [26] log likelihood: -141462.817595
EM: Round [27] log likelihood: -141462.813691
EM: Round [28] log likelihood: -141462.810488
EM: Round [29] log likelihood: -141462.807849
EM: Round [30] log likelihood: -141462.805666
EM: Round [31] log likelihood: -141462.803856
EM: Round [32] log likelihood: -141462.802349
EM: Round [33] log likelihood: -141462.801091
EM: Round [34] log likelihood: -141462.800038
EM: Round [35] log likelihood: -141462.799155
EM: Round [36] log likelihood: -141462.798412
EM: Round [37] log likelihood: -141462.797786
EM: Round [38] log likelihood: -141462.797257
EM: Round [39] log likelihood: -141462.796809
EM: Round [40] log likelihood: -141462.796430
EM: Round [41] log likelihood: -141462.796108
EM: Round [42] log likelihood: -141462.795834
EM: Round [43] log likelihood: -141462.795600
EM: Round [44] log likelihood: -141462.795401
EM: Round [45] log likelihood: -141462.795231
EM: Round [46] log likelihood: -141462.795086
EM: Round [47] log likelihood: -141462.794961
EM: Round [48] log likelihood: -141462.794855
EM: Round [49] log likelihood: -141462.794763
EM: Stopping iterations at round 49 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -141535.498327
EM: Round [1] log likelihood: -141473.491675
EM: Round [2] log likelihood: -141453.378594
EM: Round [3] log likelihood: -141444.872915
EM: Round [4] log likelihood: -141440.648910
EM: Round [5] log likelihood: -141438.329259
EM: Round [6] log likelihood: -141436.964006
EM: Round [7] log likelihood: -141436.116535
EM: Round [8] log likelihood: -141435.567074
EM: Round [9] log likelihood: -141435.197685
EM: Round [10] log likelihood: -141434.941747
EM: Round [11] log likelihood: -141434.759922
EM: Round [12] log likelihood: -141434.628038
EM: Round [13] log likelihood: -141434.530705
EM: Round [14] log likelihood: -141434.457809
EM: Round [15] log likelihood: -141434.402526
EM: Round [16] log likelihood: -141434.360140
EM: Round [17] log likelihood: -141434.327325
EM: Round [18] log likelihood: -141434.301699
EM: Round [19] log likelihood: -141434.281530
EM: Round [20] log likelihood: -141434.265542
EM: Round [21] log likelihood: -141434.252784
EM: Round [22] log likelihood: -141434.242543
EM: Round [23] log likelihood: -141434.234276
EM: Round [24] log likelihood: -141434.227568
EM: Round [25] log likelihood: -141434.222100
EM: Round [26] log likelihood: -141434.217622
EM: Round [27] log likelihood: -141434.213940
EM: Round [28] log likelihood: -141434.210902
EM: Round [29] log likelihood: -141434.208385
EM: Round [30] log likelihood: -141434.206295
EM: Round [31] log likelihood: -141434.204552
EM: Round [32] log likelihood: -141434.203097
EM: Round [33] log likelihood: -141434.201877
EM: Round [34] log likelihood: -141434.200853
EM: Round [35] log likelihood: -141434.199991
EM: Round [36] log likelihood: -141434.199264
EM: Round [37] log likelihood: -141434.198649
EM: Round [38] log likelihood: -141434.198129
EM: Round [39] log likelihood: -141434.197688
EM: Round [40] log likelihood: -141434.197314
EM: Round [41] log likelihood: -141434.196995
EM: Round [42] log likelihood: -141434.196724
EM: Round [43] log likelihood: -141434.196493
EM: Round [44] log likelihood: -141434.196295
EM: Round [45] log likelihood: -141434.196126
EM: Round [46] log likelihood: -141434.195982
EM: Round [47] log likelihood: -141434.195858
EM: Round [48] log likelihood: -141434.195752
EM: Round [49] log likelihood: -141434.195661
EM: Stopping iterations at round 49 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.riUCU57EJJ/./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.riUCU57EJJ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.riUCU57EJJ/./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.riUCU57EJJ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 116041077 > /tmp/nxf.riUCU57EJJ/./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.riUCU57EJJ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir > /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir --annotate /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.riUCU57EJJ/./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.riUCU57EJJ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir
-done, see /tmp/nxf.riUCU57EJJ/./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.riUCU57EJJ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.riUCU57EJJ/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 273, filtered: 11204)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.riUCU57EJJ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.riUCU57EJJ/./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.riUCU57EJJ/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000229739.4]
WARNING, no entry stored in dbm for [ENSG00000287721.1]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000270788.1]
WARNING, no entry stored in dbm for [ENSG00000249274.1]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000228801.6]
WARNING, no entry stored in dbm for [ENSG00000111788.10]
WARNING, no entry stored in dbm for [ENSG00000257612.2]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000234405.2]
WARNING, no entry stored in dbm for [ENSG00000287826.1]
WARNING, no entry stored in dbm for [ENSG00000286045.1]
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 [ENSG00000285758.2]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000233747.1]
WARNING, no entry stored in dbm for [ENSG00000228005.1]
WARNING, no entry stored in dbm for [ENSG00000239455.1]
WARNING, no entry stored in dbm for [ENSG00000286271.2]
WARNING, no entry stored in dbm for [ENSG00000280383.1]
WARNING, no entry stored in dbm for [ENSG00000264589.4]
WARNING, no entry stored in dbm for [ENSG00000280145.3]
WARNING, no entry stored in dbm for [ENSG00000260809.1]
WARNING, no entry stored in dbm for [ENSG00000184608.9]
WARNING, no entry stored in dbm for [ENSG00000257815.7]
WARNING, no entry stored in dbm for [ENSG00000237689.1]
WARNING, no entry stored in dbm for [ENSG00000267252.6]
WARNING, no entry stored in dbm for [ENSG00000257826.1]
WARNING, no entry stored in dbm for [ENSG00000175061.18]
WARNING, no entry stored in dbm for [ENSG00000185031.6]
WARNING, no entry stored in dbm for [ENSG00000135502.19]
WARNING, no entry stored in dbm for [ENSG00000214922.9]
WARNING, no entry stored in dbm for [ENSG00000248445.5]
WARNING, no entry stored in dbm for [ENSG00000277690.2]
WARNING, no entry stored in dbm for [ENSG00000232915.1]
WARNING, no entry stored in dbm for [ENSG00000254040.2]
WARNING, no entry stored in dbm for [ENSG00000251199.6]
WARNING, no entry stored in dbm for [ENSG00000281741.2]
WARNING, no entry stored in dbm for [ENSG00000273062.1]
WARNING, no entry stored in dbm for [ENSG00000254634.4]
WARNING, no entry stored in dbm for [ENSG00000236319.2]
WARNING, no entry stored in dbm for [ENSG00000257815.7]
WARNING, no entry stored in dbm for [ENSG00000255440.2]
WARNING, no entry stored in dbm for [ENSG00000215866.8]
WARNING, no entry stored in dbm for [ENSG00000276316.1]
WARNING, no entry stored in dbm for [ENSG00000273489.1]
WARNING, no entry stored in dbm for [ENSG00000248578.1]
WARNING, no entry stored in dbm for [ENSG00000285653.1]
WARNING, no entry stored in dbm for [ENSG00000224769.1]
WARNING, no entry stored in dbm for [ENSG00000283518.1]
WARNING, no entry stored in dbm for [ENSG00000267309.1]
WARNING, no entry stored in dbm for [ENSG00000234072.1]
WARNING, no entry stored in dbm for [ENSG00000250986.1]
WARNING, no entry stored in dbm for [ENSG00000214548.18]
WARNING, no entry stored in dbm for [ENSG00000216863.10]
WARNING, no entry stored in dbm for [ENSG00000263584.1]
WARNING, no entry stored in dbm for [ENSG00000227121.2]
WARNING, no entry stored in dbm for [ENSG00000231566.2]
WARNING, no entry stored in dbm for [ENSG00000232164.1]
WARNING, no entry stored in dbm for [ENSG00000223823.1]
WARNING, no entry stored in dbm for [ENSG00000249917.3]
WARNING, no entry stored in dbm for [ENSG00000228793.2]
WARNING, no entry stored in dbm for [ENSG00000214922.9]
WARNING, no entry stored in dbm for [ENSG00000236671.9]
WARNING, no entry stored in dbm for [ENSG00000238215.1]
WARNING, no entry stored in dbm for [ENSG00000256234.1]
WARNING, no entry stored in dbm for [ENSG00000229619.4]
WARNING, no entry stored in dbm for [ENSG00000231074.9]
WARNING, no entry stored in dbm for [ENSG00000235332.2]
WARNING, no entry stored in dbm for [ENSG00000247095.3]
WARNING, no entry stored in dbm for [ENSG00000268218.1]
WARNING, no entry stored in dbm for [ENSG00000260493.1]
WARNING, no entry stored in dbm for [ENSG00000236723.2]
WARNING, no entry stored in dbm for [ENSG00000259361.7]
WARNING, no entry stored in dbm for [ENSG00000281491.1]
WARNING, no entry stored in dbm for [ENSG00000243230.1]
WARNING, no entry stored in dbm for [ENSG00000203930.12]
WARNING, no entry stored in dbm for [ENSG00000234420.7]
WARNING, no entry stored in dbm for [ENSG00000224078.15]
WARNING, no entry stored in dbm for [ENSG00000254166.3]
WARNING, no entry stored in dbm for [ENSG00000231245.2]
WARNING, no entry stored in dbm for [ENSG00000256699.1]
WARNING, no entry stored in dbm for [ENSG00000288691.1]
WARNING, no entry stored in dbm for [ENSG00000265737.1]
WARNING, no entry stored in dbm for [ENSG00000246090.7]
WARNING, no entry stored in dbm for [ENSG00000228703.1]
WARNING, no entry stored in dbm for [ENSG00000228703.1]
WARNING, no entry stored in dbm for [ENSG00000233547.1]
WARNING, no entry stored in dbm for [ENSG00000230928.1]
WARNING, no entry stored in dbm for [ENSG00000229862.5]
WARNING, no entry stored in dbm for [ENSG00000235168.1]
WARNING, no entry stored in dbm for [ENSG00000228939.1]
WARNING, no entry stored in dbm for [ENSG00000251216.2]
WARNING, no entry stored in dbm for [ENSG00000249626.1]
WARNING, no entry stored in dbm for [ENSG00000234345.2]
WARNING, no entry stored in dbm for [ENSG00000229229.1]
WARNING, no entry stored in dbm for [ENSG00000232604.1]
WARNING, no entry stored in dbm for [ENSG00000231672.8]
WARNING, no entry stored in dbm for [ENSG00000272702.1]
WARNING, no entry stored in dbm for [ENSG00000238045.9]
WARNING, no entry stored in dbm for [ENSG00000260252.1]
WARNING, no entry stored in dbm for [ENSG00000261644.2]
* STAR-Fusion complete. See output: /tmp/nxf.riUCU57EJJ/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)