-ctat genome lib [/tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.b0B4aHNly5/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary -sample contains 9932006 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir -J /tmp/nxf.b0B4aHNly5/rna_s1221_S42.Chimeric.out.junction -O /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.b0B4aHNly5/rna_s1221_S42.Chimeric.out.junction -building interval tree based on /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.05 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=200000.00/min [30000], rate=257142.86/min [40000], rate=342857.14/min [50000], rate=300000.00/min [60000], rate=240000.00/min [70000], rate=200000.00/min [80000], rate=192000.00/min [90000], rate=192857.14/min [100000], rate=214285.71/min [110000], rate=227586.21/min [120000], rate=248275.86/min [130000], rate=236363.64/min [140000], rate=240000.00/min -building interval tree based on /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.05 min). -mapping reads to genes [10000], rate=120000.00/min [20000], rate=171428.57/min [30000], rate=200000.00/min [40000], rate=171428.57/min [50000], rate=200000.00/min [60000], rate=189473.68/min [70000], rate=161538.46/min [80000], rate=165517.24/min [90000], rate=158823.53/min [100000], rate=150000.00/min [110000], rate=160975.61/min [120000], rate=133333.33/min [130000], rate=111428.57/min -building interval tree based on /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.05 min). -mapping reads to genes [10000], rate=54545.45/min [20000], rate=92307.69/min [30000], rate=100000.00/min [40000], rate=96000.00/min [50000], rate=83333.33/min [60000], rate=81818.18/min [70000], rate=80769.23/min [80000], rate=80000.00/min [90000], rate=78260.87/min [100000], rate=77922.08/min [110000], rate=78571.43/min [120000], rate=78260.87/min [130000], rate=79591.84/min -building interval tree based on /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.05 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=57142.86/min [30000], rate=56250.00/min [40000], rate=63157.89/min [50000], rate=66666.67/min [60000], rate=69230.77/min [70000], rate=66666.67/min [80000], rate=67605.63/min [90000], rate=66666.67/min [100000], rate=68181.82/min [110000], rate=66666.67/min [120000], rate=65454.55/min [130000], rate=66666.67/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir --filt_file /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 0.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.b0B4aHNly5/rna_s1221_S42.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.b0B4aHNly5/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -23093.648792 EM: Round [1] log likelihood: -23087.484357 EM: Round [2] log likelihood: -23085.050891 EM: Round [3] log likelihood: -23083.773025 EM: Round [4] log likelihood: -23083.019702 EM: Round [5] log likelihood: -23082.544715 EM: Round [6] log likelihood: -23082.228764 EM: Round [7] log likelihood: -23082.008530 EM: Round [8] log likelihood: -23081.848638 EM: Round [9] log likelihood: -23081.728487 EM: Round [10] log likelihood: -23081.635597 EM: Round [11] log likelihood: -23081.562112 EM: Round [12] log likelihood: -23081.502898 EM: Round [13] log likelihood: -23081.454481 EM: Round [14] log likelihood: -23081.414427 EM: Round [15] log likelihood: -23081.380982 EM: Round [16] log likelihood: -23081.352846 EM: Round [17] log likelihood: -23081.329033 EM: Round [18] log likelihood: -23081.308779 EM: Round [19] log likelihood: -23081.291483 EM: Round [20] log likelihood: -23081.276662 EM: Round [21] log likelihood: -23081.263928 EM: Round [22] log likelihood: -23081.252960 EM: Round [23] log likelihood: -23081.243496 EM: Round [24] log likelihood: -23081.235316 EM: Round [25] log likelihood: -23081.228234 EM: Round [26] log likelihood: -23081.222097 EM: Round [27] log likelihood: -23081.216772 EM: Round [28] log likelihood: -23081.212149 EM: Round [29] log likelihood: -23081.208131 EM: Round [30] log likelihood: -23081.204636 EM: Round [31] log likelihood: -23081.201596 EM: Round [32] log likelihood: -23081.198949 EM: Round [33] log likelihood: -23081.196643 EM: Round [34] log likelihood: -23081.194634 EM: Round [35] log likelihood: -23081.192882 EM: Round [36] log likelihood: -23081.191355 EM: Round [37] log likelihood: -23081.190023 EM: Round [38] log likelihood: -23081.188861 EM: Round [39] log likelihood: -23081.187848 EM: Round [40] log likelihood: -23081.186963 EM: Round [41] log likelihood: -23081.186190 EM: Round [42] log likelihood: -23081.185516 EM: Round [43] log likelihood: -23081.184927 EM: Round [44] log likelihood: -23081.184412 EM: Round [45] log likelihood: -23081.183963 EM: Round [46] log likelihood: -23081.183571 EM: Round [47] log likelihood: -23081.183228 EM: Round [48] log likelihood: -23081.182928 EM: Round [49] log likelihood: -23081.182667 EM: Round [50] log likelihood: -23081.182438 EM: Round [51] log likelihood: -23081.182238 EM: Round [52] log likelihood: -23081.182064 EM: Round [53] log likelihood: -23081.181911 EM: Round [54] log likelihood: -23081.181778 EM: Round [55] log likelihood: -23081.181661 EM: Round [56] log likelihood: -23081.181559 EM: Round [57] log likelihood: -23081.181470 EM: Stopping iterations at round 57 due to insufficient improvement in likelihood. EM: Starting log likelihood: -23092.947677 EM: Round [1] log likelihood: -23087.121344 EM: Round [2] log likelihood: -23084.825823 EM: Round [3] log likelihood: -23083.616951 EM: Round [4] log likelihood: -23082.904429 EM: Round [5] log likelihood: -23082.456701 EM: Round [6] log likelihood: -23082.160382 EM: Round [7] log likelihood: -23081.954893 EM: Round [8] log likelihood: -23081.806331 EM: Round [9] log likelihood: -23081.694997 EM: Round [10] log likelihood: -23081.609021 EM: Round [11] log likelihood: -23081.540985 EM: Round [12] log likelihood: -23081.486081 EM: Round [13] log likelihood: -23081.441080 EM: Round [14] log likelihood: -23081.403740 EM: Round [15] log likelihood: -23081.372453 EM: Round [16] log likelihood: -23081.346037 EM: Round [17] log likelihood: -23081.323594 EM: Round [18] log likelihood: -23081.304434 EM: Round [19] log likelihood: -23081.288010 EM: Round [20] log likelihood: -23081.273886 EM: Round [21] log likelihood: -23081.261708 EM: Round [22] log likelihood: -23081.251186 EM: Round [23] log likelihood: -23081.242077 EM: Round [24] log likelihood: -23081.234181 EM: Round [25] log likelihood: -23081.227327 EM: Round [26] log likelihood: -23081.221371 EM: Round [27] log likelihood: -23081.216192 EM: Round [28] log likelihood: -23081.211684 EM: Round [29] log likelihood: -23081.207759 EM: Round [30] log likelihood: -23081.204339 EM: Round [31] log likelihood: -23081.201358 EM: Round [32] log likelihood: -23081.198758 EM: Round [33] log likelihood: -23081.196491 EM: Round [34] log likelihood: -23081.194512 EM: Round [35] log likelihood: -23081.192785 EM: Round [36] log likelihood: -23081.191277 EM: Round [37] log likelihood: -23081.189961 EM: Round [38] log likelihood: -23081.188812 EM: Round [39] log likelihood: -23081.187808 EM: Round [40] log likelihood: -23081.186931 EM: Round [41] log likelihood: -23081.186165 EM: Round [42] log likelihood: -23081.185495 EM: Round [43] log likelihood: -23081.184910 EM: Round [44] log likelihood: -23081.184399 EM: Round [45] log likelihood: -23081.183953 EM: Round [46] log likelihood: -23081.183562 EM: Round [47] log likelihood: -23081.183221 EM: Round [48] log likelihood: -23081.182923 EM: Round [49] log likelihood: -23081.182662 EM: Round [50] log likelihood: -23081.182435 EM: Round [51] log likelihood: -23081.182236 EM: Round [52] log likelihood: -23081.182061 EM: Round [53] log likelihood: -23081.181909 EM: Round [54] log likelihood: -23081.181776 EM: Round [55] log likelihood: -23081.181660 EM: Round [56] log likelihood: -23081.181558 EM: Round [57] log likelihood: -23081.181469 EM: Stopping iterations at round 57 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.b0B4aHNly5/./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.b0B4aHNly5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.b0B4aHNly5/./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.b0B4aHNly5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9932006 > /tmp/nxf.b0B4aHNly5/./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.b0B4aHNly5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir > /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir --annotate /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.b0B4aHNly5/./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.b0B4aHNly5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir -done, see /tmp/nxf.b0B4aHNly5/./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.b0B4aHNly5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.b0B4aHNly5/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 452, filtered: 1791) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.b0B4aHNly5/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.b0B4aHNly5/./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.b0B4aHNly5/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000180747.15] WARNING, no entry stored in dbm for [ENSG00000205534.6] WARNING, no entry stored in dbm for [ENSG00000254485.5] 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 [ENSG00000282458.1] WARNING, no entry stored in dbm for [ENSG00000236491.1] WARNING, no entry stored in dbm for [ENSG00000226520.1] WARNING, no entry stored in dbm for [ENSG00000131401.11] WARNING, no entry stored in dbm for [ENSG00000245008.4] WARNING, no entry stored in dbm for [ENSG00000165178.9] WARNING, no entry stored in dbm for [ENSG00000226419.8] WARNING, no entry stored in dbm for [ENSG00000232894.1] WARNING, no entry stored in dbm for [ENSG00000266904.6] WARNING, no entry stored in dbm for [ENSG00000286915.1] WARNING, no entry stored in dbm for [ENSG00000238061.2] WARNING, no entry stored in dbm for [ENSG00000250988.7] WARNING, no entry stored in dbm for [ENSG00000248121.8] WARNING, no entry stored in dbm for [ENSG00000250462.8] WARNING, no entry stored in dbm for [ENSG00000260727.2] WARNING, no entry stored in dbm for [ENSG00000287411.1] WARNING, no entry stored in dbm for [ENSG00000237730.1] WARNING, no entry stored in dbm for [ENSG00000253223.1] WARNING, no entry stored in dbm for [ENSG00000230559.1] WARNING, no entry stored in dbm for [ENSG00000225661.7] WARNING, no entry stored in dbm for [ENSG00000139239.7] WARNING, no entry stored in dbm for [ENSG00000274210.1] WARNING, no entry stored in dbm for [ENSG00000206975.1] WARNING, no entry stored in dbm for [ENSG00000231259.5] WARNING, no entry stored in dbm for [ENSG00000285847.2] WARNING, no entry stored in dbm for [ENSG00000173209.23] WARNING, no entry stored in dbm for [ENSG00000229502.5] WARNING, no entry stored in dbm for [ENSG00000287011.1] WARNING, no entry stored in dbm for [ENSG00000272655.2] WARNING, no entry stored in dbm for [ENSG00000223891.6] WARNING, no entry stored in dbm for [ENSG00000232422.1] WARNING, no entry stored in dbm for [ENSG00000223612.3] WARNING, no entry stored in dbm for [ENSG00000285744.1] WARNING, no entry stored in dbm for [ENSG00000206585.1] 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 [ENSG00000247675.7] WARNING, no entry stored in dbm for [ENSG00000223387.6] WARNING, no entry stored in dbm for [ENSG00000231721.7] WARNING, no entry stored in dbm for [ENSG00000244675.2] WARNING, no entry stored in dbm for [ENSG00000251301.7] WARNING, no entry stored in dbm for [ENSG00000286248.1] WARNING, no entry stored in dbm for [ENSG00000222020.3] WARNING, no entry stored in dbm for [ENSG00000220157.4] WARNING, no entry stored in dbm for [ENSG00000177410.13] WARNING, no entry stored in dbm for [ENSG00000231527.7] WARNING, no entry stored in dbm for [ENSG00000179523.5] WARNING, no entry stored in dbm for [ENSG00000244306.11] WARNING, no entry stored in dbm for [ENSG00000257222.1] WARNING, no entry stored in dbm for [ENSG00000231607.13] WARNING, no entry stored in dbm for [ENSG00000231672.8] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000231890.8] WARNING, no entry stored in dbm for [ENSG00000231421.8] WARNING, no entry stored in dbm for [ENSG00000278903.3] WARNING, no entry stored in dbm for [ENSG00000285454.1] WARNING, no entry stored in dbm for [ENSG00000254231.3] WARNING, no entry stored in dbm for [ENSG00000224216.1] WARNING, no entry stored in dbm for [ENSG00000246985.8] WARNING, no entry stored in dbm for [ENSG00000270714.1] WARNING, no entry stored in dbm for [ENSG00000229807.12] WARNING, no entry stored in dbm for [ENSG00000229956.11] WARNING, no entry stored in dbm for [ENSG00000158483.17] WARNING, no entry stored in dbm for [ENSG00000228436.3] WARNING, no entry stored in dbm for [ENSG00000227486.2] WARNING, no entry stored in dbm for [ENSG00000274760.1] WARNING, no entry stored in dbm for [ENSG00000232855.7] WARNING, no entry stored in dbm for [ENSG00000277125.1] WARNING, no entry stored in dbm for [ENSG00000286830.1] WARNING, no entry stored in dbm for [ENSG00000277125.1] WARNING, no entry stored in dbm for [ENSG00000286830.1] WARNING, no entry stored in dbm for [ENSG00000227077.3] WARNING, no entry stored in dbm for [ENSG00000225159.1] WARNING, no entry stored in dbm for [ENSG00000284669.1] WARNING, no entry stored in dbm for [ENSG00000239969.5] WARNING, no entry stored in dbm for [ENSG00000286011.1] WARNING, no entry stored in dbm for [ENSG00000259772.6] WARNING, no entry stored in dbm for [ENSG00000248540.3] WARNING, no entry stored in dbm for [ENSG00000230383.1] WARNING, no entry stored in dbm for [ENSG00000257403.2] WARNING, no entry stored in dbm for [ENSG00000189149.12] WARNING, no entry stored in dbm for [ENSG00000269968.1] WARNING, no entry stored in dbm for [ENSG00000243004.6] WARNING, no entry stored in dbm for [ENSG00000265206.5] WARNING, no entry stored in dbm for [ENSG00000237296.9] * STAR-Fusion complete. See output: /tmp/nxf.b0B4aHNly5/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)