-ctat genome lib [/tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.mMHlTwZpc9/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary -sample contains 698690 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir -J /tmp/nxf.mMHlTwZpc9/aih-tih-sc-331e97-R1_A23WJ53LT4_1.Chimeric.out.junction -O /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.mMHlTwZpc9/aih-tih-sc-331e97-R1_A23WJ53LT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.mMHlTwZpc9/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 -building interval tree based on /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=54545.45/min -building interval tree based on /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=54545.45/min -building interval tree based on /tmp/nxf.mMHlTwZpc9/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 * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir --filt_file /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.mMHlTwZpc9/aih-tih-sc-331e97-R1_A23WJ53LT4_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.mMHlTwZpc9/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -1128.259930 EM: Round [1] log likelihood: -1127.619008 EM: Round [2] log likelihood: -1127.384714 EM: Round [3] log likelihood: -1127.283659 EM: Round [4] log likelihood: -1127.236538 EM: Round [5] log likelihood: -1127.212797 EM: Round [6] log likelihood: -1127.199682 EM: Round [7] log likelihood: -1127.191582 EM: Round [8] log likelihood: -1127.185939 EM: Round [9] log likelihood: -1127.181558 EM: Round [10] log likelihood: -1127.177872 EM: Round [11] log likelihood: -1127.174610 EM: Round [12] log likelihood: -1127.171642 EM: Round [13] log likelihood: -1127.168905 EM: Round [14] log likelihood: -1127.166370 EM: Round [15] log likelihood: -1127.164018 EM: Round [16] log likelihood: -1127.161841 EM: Round [17] log likelihood: -1127.159830 EM: Round [18] log likelihood: -1127.157979 EM: Round [19] log likelihood: -1127.156279 EM: Round [20] log likelihood: -1127.154723 EM: Round [21] log likelihood: -1127.153303 EM: Round [22] log likelihood: -1127.152010 EM: Round [23] log likelihood: -1127.150835 EM: Round [24] log likelihood: -1127.149771 EM: Round [25] log likelihood: -1127.148808 EM: Round [26] log likelihood: -1127.147939 EM: Round [27] log likelihood: -1127.147156 EM: Round [28] log likelihood: -1127.146451 EM: Round [29] log likelihood: -1127.145817 EM: Round [30] log likelihood: -1127.145248 EM: Round [31] log likelihood: -1127.144738 EM: Round [32] log likelihood: -1127.144281 EM: Round [33] log likelihood: -1127.143871 EM: Round [34] log likelihood: -1127.143505 EM: Round [35] log likelihood: -1127.143178 EM: Round [36] log likelihood: -1127.142886 EM: Round [37] log likelihood: -1127.142624 EM: Round [38] log likelihood: -1127.142392 EM: Round [39] log likelihood: -1127.142184 EM: Round [40] log likelihood: -1127.141998 EM: Round [41] log likelihood: -1127.141833 EM: Round [42] log likelihood: -1127.141686 EM: Round [43] log likelihood: -1127.141555 EM: Round [44] log likelihood: -1127.141438 EM: Round [45] log likelihood: -1127.141334 EM: Round [46] log likelihood: -1127.141241 EM: Stopping iterations at round 46 due to insufficient improvement in likelihood. EM: Starting log likelihood: -1128.138774 EM: Round [1] log likelihood: -1127.567580 EM: Round [2] log likelihood: -1127.359583 EM: Round [3] log likelihood: -1127.270195 EM: Round [4] log likelihood: -1127.228604 EM: Round [5] log likelihood: -1127.207581 EM: Round [6] log likelihood: -1127.195844 EM: Round [7] log likelihood: -1127.188472 EM: Round [8] log likelihood: -1127.183242 EM: Round [9] log likelihood: -1127.179121 EM: Round [10] log likelihood: -1127.175623 EM: Round [11] log likelihood: -1127.172514 EM: Round [12] log likelihood: -1127.169684 EM: Round [13] log likelihood: -1127.167078 EM: Round [14] log likelihood: -1127.164668 EM: Round [15] log likelihood: -1127.162439 EM: Round [16] log likelihood: -1127.160380 EM: Round [17] log likelihood: -1127.158483 EM: Round [18] log likelihood: -1127.156741 EM: Round [19] log likelihood: -1127.155145 EM: Round [20] log likelihood: -1127.153688 EM: Round [21] log likelihood: -1127.152360 EM: Round [22] log likelihood: -1127.151153 EM: Round [23] log likelihood: -1127.150059 EM: Round [24] log likelihood: -1127.149068 EM: Round [25] log likelihood: -1127.148174 EM: Round [26] log likelihood: -1127.147367 EM: Round [27] log likelihood: -1127.146641 EM: Round [28] log likelihood: -1127.145988 EM: Round [29] log likelihood: -1127.145401 EM: Round [30] log likelihood: -1127.144875 EM: Round [31] log likelihood: -1127.144404 EM: Round [32] log likelihood: -1127.143982 EM: Round [33] log likelihood: -1127.143604 EM: Round [34] log likelihood: -1127.143266 EM: Round [35] log likelihood: -1127.142964 EM: Round [36] log likelihood: -1127.142695 EM: Round [37] log likelihood: -1127.142454 EM: Round [38] log likelihood: -1127.142240 EM: Round [39] log likelihood: -1127.142048 EM: Round [40] log likelihood: -1127.141878 EM: Round [41] log likelihood: -1127.141726 EM: Round [42] log likelihood: -1127.141590 EM: Round [43] log likelihood: -1127.141469 EM: Round [44] log likelihood: -1127.141362 EM: Round [45] log likelihood: -1127.141266 EM: Stopping iterations at round 45 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 698690 > /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir > /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir --annotate /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir -done, see /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.mMHlTwZpc9/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 23, filtered: 272) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.mMHlTwZpc9/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.mMHlTwZpc9/./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.mMHlTwZpc9/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 [ENSG00000251562.8] WARNING, no entry stored in dbm for [ENSG00000251562.8] WARNING, no entry stored in dbm for [ENSG00000260735.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000233955.1] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000203413.3] WARNING, no entry stored in dbm for [ENSG00000260236.1] * STAR-Fusion complete. See output: /tmp/nxf.mMHlTwZpc9/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)