-ctat genome lib [/tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.lUNqPHBMJD/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary -sample contains 149272 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir -J /tmp/nxf.lUNqPHBMJD/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction -O /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.lUNqPHBMJD/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction -building interval tree based on /tmp/nxf.lUNqPHBMJD/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=62068.97/min [40000], rate=64864.86/min [50000], rate=68181.82/min -building interval tree based on /tmp/nxf.lUNqPHBMJD/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=60000.00/min [30000], rate=56250.00/min [40000], rate=61538.46/min [50000], rate=61224.49/min -building interval tree based on /tmp/nxf.lUNqPHBMJD/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 [20000], rate=54545.45/min [30000], rate=50000.00/min [40000], rate=52173.91/min [50000], rate=55555.56/min -building interval tree based on /tmp/nxf.lUNqPHBMJD/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 [20000], rate=66666.67/min [30000], rate=60000.00/min [40000], rate=58536.59/min [50000], rate=56603.77/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir --filt_file /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 6000000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.lUNqPHBMJD/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.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.lUNqPHBMJD/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -1219.612376 EM: Round [1] log likelihood: -1217.733801 EM: Round [2] log likelihood: -1217.106687 EM: Round [3] log likelihood: -1216.841563 EM: Round [4] log likelihood: -1216.712217 EM: Round [5] log likelihood: -1216.642717 EM: Round [6] log likelihood: -1216.602437 EM: Round [7] log likelihood: -1216.577539 EM: Round [8] log likelihood: -1216.561284 EM: Round [9] log likelihood: -1216.550182 EM: Round [10] log likelihood: -1216.542324 EM: Round [11] log likelihood: -1216.536607 EM: Round [12] log likelihood: -1216.532360 EM: Round [13] log likelihood: -1216.529157 EM: Round [14] log likelihood: -1216.526711 EM: Round [15] log likelihood: -1216.524827 EM: Round [16] log likelihood: -1216.523366 EM: Round [17] log likelihood: -1216.522226 EM: Round [18] log likelihood: -1216.521333 EM: Round [19] log likelihood: -1216.520632 EM: Round [20] log likelihood: -1216.520079 EM: Round [21] log likelihood: -1216.519641 EM: Round [22] log likelihood: -1216.519295 EM: Round [23] log likelihood: -1216.519021 EM: Round [24] log likelihood: -1216.518803 EM: Round [25] log likelihood: -1216.518629 EM: Round [26] log likelihood: -1216.518491 EM: Round [27] log likelihood: -1216.518381 EM: Round [28] log likelihood: -1216.518294 EM: Stopping iterations at round 28 due to insufficient improvement in likelihood. EM: Starting log likelihood: -1219.259027 EM: Round [1] log likelihood: -1217.606122 EM: Round [2] log likelihood: -1217.057506 EM: Round [3] log likelihood: -1216.822176 EM: Round [4] log likelihood: -1216.704508 EM: Round [5] log likelihood: -1216.639640 EM: Round [6] log likelihood: -1216.601207 EM: Round [7] log likelihood: -1216.577048 EM: Round [8] log likelihood: -1216.561088 EM: Round [9] log likelihood: -1216.550104 EM: Round [10] log likelihood: -1216.542292 EM: Round [11] log likelihood: -1216.536594 EM: Round [12] log likelihood: -1216.532355 EM: Round [13] log likelihood: -1216.529155 EM: Round [14] log likelihood: -1216.526710 EM: Round [15] log likelihood: -1216.524827 EM: Round [16] log likelihood: -1216.523366 EM: Round [17] log likelihood: -1216.522226 EM: Round [18] log likelihood: -1216.521333 EM: Round [19] log likelihood: -1216.520632 EM: Round [20] log likelihood: -1216.520079 EM: Round [21] log likelihood: -1216.519641 EM: Round [22] log likelihood: -1216.519295 EM: Round [23] log likelihood: -1216.519021 EM: Round [24] log likelihood: -1216.518803 EM: Round [25] log likelihood: -1216.518629 EM: Round [26] log likelihood: -1216.518491 EM: Round [27] log likelihood: -1216.518381 EM: Round [28] log likelihood: -1216.518294 EM: Stopping iterations at round 28 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 149272 > /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir > /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir --annotate /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir -done, see /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.lUNqPHBMJD/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 15, filtered: 232) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.lUNqPHBMJD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.lUNqPHBMJD/./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.lUNqPHBMJD/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 [ENSG00000227195.11] WARNING, no entry stored in dbm for [ENSG00000257167.2] WARNING, no entry stored in dbm for [ENSG00000223823.1] WARNING, no entry stored in dbm for [ENSG00000262151.1] WARNING, no entry stored in dbm for [ENSG00000223823.1] WARNING, no entry stored in dbm for [ENSG00000262151.1] 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 [ENSG00000274021.1] 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 [ENSG00000228422.5] WARNING, no entry stored in dbm for [ENSG00000205485.13] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000230676.1] WARNING, no entry stored in dbm for [IGH-.g@-ext] * STAR-Fusion complete. See output: /tmp/nxf.lUNqPHBMJD/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)