-ctat genome lib [/tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.0kmkuWaYEo/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary
-sample contains 1433549 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir  -J /tmp/nxf.0kmkuWaYEo/OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.0kmkuWaYEo/OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=66666.67/min 
[20000], rate=75000.00/min 
[30000], rate=72000.00/min 
[40000], rate=70588.24/min 
[50000], rate=69767.44/min 
[60000], rate=70588.24/min 
[70000], rate=72413.79/min 
[80000], rate=71641.79/min 
[90000], rate=72000.00/min 
[100000], rate=71428.57/min 
[110000], rate=67346.94/min 
[120000], rate=66666.67/min 
[130000], rate=66666.67/min 
[140000], rate=66141.73/min 
[150000], rate=67164.18/min -building interval tree based on /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=60000.00/min 
[20000], rate=60000.00/min 
[30000], rate=66666.67/min 
[40000], rate=61538.46/min 
[50000], rate=63829.79/min 
[60000], rate=66666.67/min 
[70000], rate=62686.57/min 
[80000], rate=62337.66/min 
[90000], rate=62790.70/min 
[100000], rate=63157.89/min 
[110000], rate=62857.14/min 
[120000], rate=63716.81/min 
[130000], rate=65000.00/min 
[140000], rate=65625.00/min 
[150000], rate=66176.47/min -building interval tree based on /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=100000.00/min 
[20000], rate=100000.00/min 
[30000], rate=85714.29/min 
[40000], rate=82758.62/min 
[50000], rate=85714.29/min 
[60000], rate=85714.29/min 
[70000], rate=73684.21/min 
[80000], rate=64864.86/min 
[90000], rate=62068.97/min 
[100000], rate=63829.79/min 
[110000], rate=63461.54/min 
[120000], rate=64285.71/min 
[130000], rate=62903.23/min 
[140000], rate=62686.57/min 
[150000], rate=63829.79/min -building interval tree based on /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=50000.00/min 
[20000], rate=57142.86/min 
[30000], rate=62068.97/min 
[40000], rate=66666.67/min 
[50000], rate=69767.44/min 
[60000], rate=70588.24/min 
[70000], rate=71186.44/min 
[80000], rate=68571.43/min 
[90000], rate=67500.00/min 
[100000], rate=64516.13/min 
[110000], rate=66000.00/min 
[120000], rate=64864.86/min 
[130000], rate=63934.43/min 
[140000], rate=61313.87/min 
[150000], rate=60000.00/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.0kmkuWaYEo/./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...  
 4500000.00 reads per min processed...  
 4800000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.0kmkuWaYEo/OvarianN_FFPE_L03_RNA_01_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.0kmkuWaYEo/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -6335.803757
EM: Round [1] log likelihood: -6329.184551
EM: Round [2] log likelihood: -6326.005548
EM: Round [3] log likelihood: -6324.152571
EM: Round [4] log likelihood: -6323.058852
EM: Round [5] log likelihood: -6322.414706
EM: Round [6] log likelihood: -6322.031045
EM: Round [7] log likelihood: -6321.797489
EM: Round [8] log likelihood: -6321.651627
EM: Round [9] log likelihood: -6321.558232
EM: Round [10] log likelihood: -6321.497077
EM: Round [11] log likelihood: -6321.456246
EM: Round [12] log likelihood: -6321.428523
EM: Round [13] log likelihood: -6321.409427
EM: Round [14] log likelihood: -6321.396107
EM: Round [15] log likelihood: -6321.386714
EM: Round [16] log likelihood: -6321.380024
EM: Round [17] log likelihood: -6321.375218
EM: Round [18] log likelihood: -6321.371737
EM: Round [19] log likelihood: -6321.369199
EM: Round [20] log likelihood: -6321.367336
EM: Round [21] log likelihood: -6321.365960
EM: Round [22] log likelihood: -6321.364938
EM: Round [23] log likelihood: -6321.364175
EM: Round [24] log likelihood: -6321.363603
EM: Round [25] log likelihood: -6321.363172
EM: Round [26] log likelihood: -6321.362846
EM: Round [27] log likelihood: -6321.362599
EM: Round [28] log likelihood: -6321.362410
EM: Round [29] log likelihood: -6321.362266
EM: Round [30] log likelihood: -6321.362156
EM: Round [31] log likelihood: -6321.362071
EM: Stopping iterations at round 31 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -6334.469790
EM: Round [1] log likelihood: -6328.328221
EM: Round [2] log likelihood: -6325.461485
EM: Round [3] log likelihood: -6323.834260
EM: Round [4] log likelihood: -6322.883152
EM: Round [5] log likelihood: -6322.320434
EM: Round [6] log likelihood: -6321.980811
EM: Round [7] log likelihood: -6321.770557
EM: Round [8] log likelihood: -6321.636990
EM: Round [9] log likelihood: -6321.550138
EM: Round [10] log likelihood: -6321.492515
EM: Round [11] log likelihood: -6321.453625
EM: Round [12] log likelihood: -6321.426991
EM: Round [13] log likelihood: -6321.408517
EM: Round [14] log likelihood: -6321.395559
EM: Round [15] log likelihood: -6321.386380
EM: Round [16] log likelihood: -6321.379820
EM: Round [17] log likelihood: -6321.375092
EM: Round [18] log likelihood: -6321.371661
EM: Round [19] log likelihood: -6321.369152
EM: Round [20] log likelihood: -6321.367308
EM: Round [21] log likelihood: -6321.365943
EM: Round [22] log likelihood: -6321.364928
EM: Round [23] log likelihood: -6321.364170
EM: Round [24] log likelihood: -6321.363600
EM: Round [25] log likelihood: -6321.363171
EM: Round [26] log likelihood: -6321.362846
EM: Round [27] log likelihood: -6321.362599
EM: Round [28] log likelihood: -6321.362411
EM: Round [29] log likelihood: -6321.362267
EM: Round [30] log likelihood: -6321.362156
EM: Round [31] log likelihood: -6321.362071
EM: Stopping iterations at round 31 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.0kmkuWaYEo/./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.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.0kmkuWaYEo/./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.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 1433549 > /tmp/nxf.0kmkuWaYEo/./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.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir > /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir --annotate /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.0kmkuWaYEo/./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.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir
-done, see /tmp/nxf.0kmkuWaYEo/./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.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 61, filtered: 1013)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.0kmkuWaYEo/./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.0kmkuWaYEo/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 [ENSG00000213742.7]
WARNING, no entry stored in dbm for [ENSG00000197558.13]
WARNING, no entry stored in dbm for [ENSG00000286176.2]
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 [ENSG00000230461.9]
WARNING, no entry stored in dbm for [ENSG00000272078.1]
WARNING, no entry stored in dbm for [ENSG00000230426.4]
WARNING, no entry stored in dbm for [IGL-.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 [ENSG00000228422.5]
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 [ENSG00000226043.2]
WARNING, no entry stored in dbm for [ENSG00000287531.1]
WARNING, no entry stored in dbm for [ENSG00000260046.1]
WARNING, no entry stored in dbm for [ENSG00000255811.1]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000259116.2]
WARNING, no entry stored in dbm for [ENSG00000250746.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000260807.7]
WARNING, no entry stored in dbm for [ENSG00000284707.2]
WARNING, no entry stored in dbm for [ENSG00000286218.2]


	* STAR-Fusion complete.  See output: /tmp/nxf.0kmkuWaYEo/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)