Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/859affff1430540fccc8497d2ce345/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/859affff1430540fccc8497d2ce345/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/db4a0c4c037910b4fdcbb09ccd8363/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/9fbeb399ad8501a1dfe1c2c262afd7/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/9fbeb399ad8501a1dfe1c2c262afd7/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.aD9ZHTmUtE/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary -sample contains 13685877 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir -J /tmp/nxf.aD9ZHTmUtE/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.aD9ZHTmUtE/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=92307.69/min [30000], rate=75000.00/min [40000], rate=54545.45/min [50000], rate=52631.58/min [60000], rate=50704.23/min [70000], rate=45161.29/min [80000], rate=44444.44/min [90000], rate=44262.30/min [100000], rate=40000.00/min [110000], rate=37078.65/min [120000], rate=36180.90/min [130000], rate=36111.11/min [140000], rate=36681.22/min [150000], rate=37037.04/min [160000], rate=36090.23/min [170000], rate=34931.51/min [180000], rate=34951.46/min [190000], rate=35076.92/min [200000], rate=34883.72/min [210000], rate=34903.05/min [220000], rate=35483.87/min [230000], rate=36031.33/min [240000], rate=36180.90/min [250000], rate=36407.77/min [260000], rate=36448.60/min [270000], rate=36486.49/min [280000], rate=36206.90/min [290000], rate=35510.20/min [300000], rate=35714.29/min [310000], rate=35769.23/min [320000], rate=35887.85/min [330000], rate=36531.37/min [340000], rate=37294.33/min [350000], rate=37366.55/min [360000], rate=37828.37/min [370000], rate=38209.98/min [380000], rate=38578.68/min [390000], rate=39130.43/min [400000], rate=39735.10/min -building interval tree based on /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=24000.00/min [20000], rate=24489.80/min [30000], rate=27692.31/min [40000], rate=27586.21/min [50000], rate=29126.21/min [60000], rate=29752.07/min [70000], rate=30434.78/min [80000], rate=32432.43/min [90000], rate=33540.37/min [100000], rate=34482.76/min [110000], rate=35869.57/min [120000], rate=36180.90/min [130000], rate=37681.16/min [140000], rate=38009.05/min [150000], rate=38297.87/min [160000], rate=38247.01/min [170000], rate=37362.64/min [180000], rate=36486.49/min [190000], rate=37377.05/min [200000], rate=38216.56/min [210000], rate=39252.34/min [220000], rate=39759.04/min [230000], rate=40350.88/min [240000], rate=40677.97/min [250000], rate=40871.93/min [260000], rate=41379.31/min [270000], rate=41752.58/min [280000], rate=41379.31/min [290000], rate=41330.17/min [300000], rate=40909.09/min [310000], rate=39574.47/min [320000], rate=38554.22/min [330000], rate=38372.09/min [340000], rate=38636.36/min [350000], rate=38391.22/min [360000], rate=38502.67/min [370000], rate=38879.16/min [380000], rate=38907.85/min [390000], rate=39130.43/min [400000], rate=39279.87/min -building interval tree based on /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=33333.33/min [20000], rate=41379.31/min [30000], rate=45000.00/min [40000], rate=48979.59/min [50000], rate=50847.46/min [60000], rate=53731.34/min [70000], rate=53164.56/min [80000], rate=48484.85/min [90000], rate=46153.85/min [100000], rate=47244.09/min [110000], rate=45833.33/min [120000], rate=43636.36/min [130000], rate=42857.14/min [140000], rate=43076.92/min [150000], rate=44334.98/min [160000], rate=41201.72/min [170000], rate=40637.45/min [180000], rate=39130.43/min [190000], rate=38255.03/min [200000], rate=37383.18/min [210000], rate=37058.82/min [220000], rate=37183.10/min [230000], rate=36702.13/min [240000], rate=35207.82/min [250000], rate=34562.21/min [260000], rate=34589.80/min [270000], rate=34322.03/min [280000], rate=33667.33/min [290000], rate=33720.93/min [300000], rate=34026.47/min [310000], rate=34317.34/min [320000], rate=34594.59/min [330000], rate=34554.97/min [340000], rate=34517.77/min [350000], rate=34653.47/min [360000], rate=34838.71/min [370000], rate=35238.10/min [380000], rate=35736.68/min [390000], rate=36335.40/min [400000], rate=36529.68/min -building interval tree based on /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=75000.00/min [30000], rate=90000.00/min [40000], rate=92307.69/min [50000], rate=90909.09/min [60000], rate=85714.29/min [70000], rate=87500.00/min [80000], rate=90566.04/min [90000], rate=90000.00/min [100000], rate=88235.29/min [110000], rate=86842.11/min [120000], rate=82758.62/min [130000], rate=82105.26/min [140000], rate=82352.94/min [150000], rate=69230.77/min [160000], rate=53932.58/min [170000], rate=44541.48/min [180000], rate=39416.06/min [190000], rate=36655.95/min [200000], rate=34985.42/min [210000], rate=33962.26/min [220000], rate=33165.83/min [230000], rate=33333.33/min [240000], rate=33333.33/min [250000], rate=33482.14/min [260000], rate=32980.97/min [270000], rate=32595.57/min [280000], rate=33005.89/min [290000], rate=33269.60/min [300000], rate=33834.59/min [310000], rate=34191.18/min [320000], rate=33333.33/min [330000], rate=33502.54/min [340000], rate=33442.62/min [350000], rate=33653.85/min [360000], rate=34123.22/min [370000], rate=34741.78/min [380000], rate=35294.12/min [390000], rate=35562.31/min [400000], rate=35928.14/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir --filt_file /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.aD9ZHTmUtE/./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... 4500000.00 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... 4000000.00 reads per min processed... 4153846.15 reads per min processed... 4285714.29 reads per min processed... 4400000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.aD9ZHTmUtE/EndoN_FFPE_L02_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.aD9ZHTmUtE/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -27096.406876 EM: Round [1] log likelihood: -27056.303896 EM: Round [2] log likelihood: -27038.004018 EM: Round [3] log likelihood: -27028.240310 EM: Round [4] log likelihood: -27022.818679 EM: Round [5] log likelihood: -27019.773666 EM: Round [6] log likelihood: -27018.031971 EM: Round [7] log likelihood: -27017.005495 EM: Round [8] log likelihood: -27016.377418 EM: Round [9] log likelihood: -27015.977252 EM: Round [10] log likelihood: -27015.711855 EM: Round [11] log likelihood: -27015.529034 EM: Round [12] log likelihood: -27015.398637 EM: Round [13] log likelihood: -27015.302666 EM: Round [14] log likelihood: -27015.230027 EM: Round [15] log likelihood: -27015.173667 EM: Round [16] log likelihood: -27015.128967 EM: Round [17] log likelihood: -27015.092823 EM: Round [18] log likelihood: -27015.063095 EM: Round [19] log likelihood: -27015.038278 EM: Round [20] log likelihood: -27015.017289 EM: Round [21] log likelihood: -27014.999336 EM: Round [22] log likelihood: -27014.983828 EM: Round [23] log likelihood: -27014.970318 EM: Round [24] log likelihood: -27014.958462 EM: Round [25] log likelihood: -27014.947991 EM: Round [26] log likelihood: -27014.938694 EM: Round [27] log likelihood: -27014.930399 EM: Round [28] log likelihood: -27014.922968 EM: Round [29] log likelihood: -27014.916287 EM: Round [30] log likelihood: -27014.910263 EM: Round [31] log likelihood: -27014.904816 EM: Round [32] log likelihood: -27014.899878 EM: Round [33] log likelihood: -27014.895394 EM: Round [34] log likelihood: -27014.891313 EM: Round [35] log likelihood: -27014.887593 EM: Round [36] log likelihood: -27014.884199 EM: Round [37] log likelihood: -27014.881096 EM: Round [38] log likelihood: -27014.878256 EM: Round [39] log likelihood: -27014.875655 EM: Round [40] log likelihood: -27014.873270 EM: Round [41] log likelihood: -27014.871081 EM: Round [42] log likelihood: -27014.869071 EM: Round [43] log likelihood: -27014.867223 EM: Round [44] log likelihood: -27014.865523 EM: Round [45] log likelihood: -27014.863958 EM: Round [46] log likelihood: -27014.862517 EM: Round [47] log likelihood: -27014.861189 EM: Round [48] log likelihood: -27014.859964 EM: Round [49] log likelihood: -27014.858835 EM: Round [50] log likelihood: -27014.857792 EM: Round [51] log likelihood: -27014.856830 EM: Round [52] log likelihood: -27014.855940 EM: Round [53] log likelihood: -27014.855118 EM: Round [54] log likelihood: -27014.854359 EM: Round [55] log likelihood: -27014.853656 EM: Round [56] log likelihood: -27014.853006 EM: Round [57] log likelihood: -27014.852404 EM: Round [58] log likelihood: -27014.851847 EM: Round [59] log likelihood: -27014.851331 EM: Round [60] log likelihood: -27014.850852 EM: Round [61] log likelihood: -27014.850409 EM: Round [62] log likelihood: -27014.849998 EM: Round [63] log likelihood: -27014.849617 EM: Round [64] log likelihood: -27014.849264 EM: Round [65] log likelihood: -27014.848936 EM: Round [66] log likelihood: -27014.848632 EM: Round [67] log likelihood: -27014.848349 EM: Round [68] log likelihood: -27014.848087 EM: Round [69] log likelihood: -27014.847843 EM: Round [70] log likelihood: -27014.847616 EM: Round [71] log likelihood: -27014.847406 EM: Round [72] log likelihood: -27014.847210 EM: Round [73] log likelihood: -27014.847028 EM: Round [74] log likelihood: -27014.846858 EM: Round [75] log likelihood: -27014.846701 EM: Round [76] log likelihood: -27014.846554 EM: Round [77] log likelihood: -27014.846418 EM: Round [78] log likelihood: -27014.846291 EM: Round [79] log likelihood: -27014.846172 EM: Round [80] log likelihood: -27014.846062 EM: Round [81] log likelihood: -27014.845959 EM: Round [82] log likelihood: -27014.845863 EM: Stopping iterations at round 82 due to insufficient improvement in likelihood. EM: Starting log likelihood: -27088.385922 EM: Round [1] log likelihood: -27051.306744 EM: Round [2] log likelihood: -27034.902243 EM: Round [3] log likelihood: -27026.351600 EM: Round [4] log likelihood: -27021.679907 EM: Round [5] log likelihood: -27019.081357 EM: Round [6] log likelihood: -27017.601640 EM: Round [7] log likelihood: -27016.730030 EM: Round [8] log likelihood: -27016.195455 EM: Round [9] log likelihood: -27015.853322 EM: Round [10] log likelihood: -27015.625018 EM: Round [11] log likelihood: -27015.466589 EM: Round [12] log likelihood: -27015.352655 EM: Round [13] log likelihood: -27015.268058 EM: Round [14] log likelihood: -27015.203442 EM: Round [15] log likelihood: -27015.152847 EM: Round [16] log likelihood: -27015.112361 EM: Round [17] log likelihood: -27015.079347 EM: Round [18] log likelihood: -27015.051981 EM: Round [19] log likelihood: -27015.028973 EM: Round [20] log likelihood: -27015.009392 EM: Round [21] log likelihood: -27014.992552 EM: Round [22] log likelihood: -27014.977937 EM: Round [23] log likelihood: -27014.965154 EM: Round [24] log likelihood: -27014.953900 EM: Round [25] log likelihood: -27014.943933 EM: Round [26] log likelihood: -27014.935064 EM: Round [27] log likelihood: -27014.927138 EM: Round [28] log likelihood: -27014.920026 EM: Round [29] log likelihood: -27014.913627 EM: Round [30] log likelihood: -27014.907850 EM: Round [31] log likelihood: -27014.902623 EM: Round [32] log likelihood: -27014.897883 EM: Round [33] log likelihood: -27014.893576 EM: Round [34] log likelihood: -27014.889656 EM: Round [35] log likelihood: -27014.886081 EM: Round [36] log likelihood: -27014.882818 EM: Round [37] log likelihood: -27014.879835 EM: Round [38] log likelihood: -27014.877105 EM: Round [39] log likelihood: -27014.874603 EM: Round [40] log likelihood: -27014.872309 EM: Round [41] log likelihood: -27014.870203 EM: Round [42] log likelihood: -27014.868268 EM: Round [43] log likelihood: -27014.866489 EM: Round [44] log likelihood: -27014.864852 EM: Round [45] log likelihood: -27014.863346 EM: Round [46] log likelihood: -27014.861957 EM: Round [47] log likelihood: -27014.860678 EM: Round [48] log likelihood: -27014.859498 EM: Round [49] log likelihood: -27014.858408 EM: Round [50] log likelihood: -27014.857403 EM: Round [51] log likelihood: -27014.856474 EM: Round [52] log likelihood: -27014.855616 EM: Round [53] log likelihood: -27014.854822 EM: Round [54] log likelihood: -27014.854088 EM: Round [55] log likelihood: -27014.853409 EM: Round [56] log likelihood: -27014.852780 EM: Round [57] log likelihood: -27014.852198 EM: Round [58] log likelihood: -27014.851659 EM: Round [59] log likelihood: -27014.851160 EM: Round [60] log likelihood: -27014.850697 EM: Round [61] log likelihood: -27014.850267 EM: Round [62] log likelihood: -27014.849869 EM: Round [63] log likelihood: -27014.849499 EM: Round [64] log likelihood: -27014.849156 EM: Round [65] log likelihood: -27014.848838 EM: Round [66] log likelihood: -27014.848542 EM: Round [67] log likelihood: -27014.848267 EM: Round [68] log likelihood: -27014.848012 EM: Round [69] log likelihood: -27014.847775 EM: Round [70] log likelihood: -27014.847554 EM: Round [71] log likelihood: -27014.847349 EM: Round [72] log likelihood: -27014.847159 EM: Round [73] log likelihood: -27014.846981 EM: Round [74] log likelihood: -27014.846816 EM: Round [75] log likelihood: -27014.846662 EM: Round [76] log likelihood: -27014.846519 EM: Round [77] log likelihood: -27014.846386 EM: Round [78] log likelihood: -27014.846261 EM: Round [79] log likelihood: -27014.846146 EM: Round [80] log likelihood: -27014.846038 EM: Round [81] log likelihood: -27014.845937 EM: Round [82] log likelihood: -27014.845844 EM: Stopping iterations at round 82 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.aD9ZHTmUtE/./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.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.aD9ZHTmUtE/./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.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 13685877 > /tmp/nxf.aD9ZHTmUtE/./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.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir > /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir --annotate /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.aD9ZHTmUtE/./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.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir -done, see /tmp/nxf.aD9ZHTmUtE/./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.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.aD9ZHTmUtE/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 223, filtered: 2590) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.aD9ZHTmUtE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.aD9ZHTmUtE/./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.aD9ZHTmUtE/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 [ENSG00000239268.3] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000241469.9] WARNING, no entry stored in dbm for [ENSG00000267296.2] WARNING, no entry stored in dbm for [ENSG00000261423.1] WARNING, no entry stored in dbm for [ENSG00000222976.1] WARNING, no entry stored in dbm for [ENSG00000228862.4] WARNING, no entry stored in dbm for [ENSG00000241316.8] WARNING, no entry stored in dbm for [ENSG00000275549.1] WARNING, no entry stored in dbm for [ENSG00000285987.1] WARNING, no entry stored in dbm for [ENSG00000158482.10] WARNING, no entry stored in dbm for [ENSG00000276721.1] WARNING, no entry stored in dbm for [ENSG00000182776.4] WARNING, no entry stored in dbm for [ENSG00000248727.6] WARNING, no entry stored in dbm for [ENSG00000227210.2] WARNING, no entry stored in dbm for [ENSG00000279583.1] WARNING, no entry stored in dbm for [ENSG00000224081.9] WARNING, no entry stored in dbm for [ENSG00000204044.6] WARNING, no entry stored in dbm for [ENSG00000245958.6] WARNING, no entry stored in dbm for [ENSG00000185986.12] WARNING, no entry stored in dbm for [ENSG00000188002.10] WARNING, no entry stored in dbm for [ENSG00000225482.1] WARNING, no entry stored in dbm for [ENSG00000216866.5] WARNING, no entry stored in dbm for [ENSG00000262943.7] WARNING, no entry stored in dbm for [ENSG00000204745.4] WARNING, no entry stored in dbm for [ENSG00000218018.3] WARNING, no entry stored in dbm for [ENSG00000213300.5] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000259275.4] WARNING, no entry stored in dbm for [ENSG00000270231.4] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000286176.2] WARNING, no entry stored in dbm for [ENSG00000283426.1] WARNING, no entry stored in dbm for [ENSG00000186715.11] WARNING, no entry stored in dbm for [ENSG00000234474.3] WARNING, no entry stored in dbm for [ENSG00000260738.1] WARNING, no entry stored in dbm for [ENSG00000236432.8] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000232527.8] WARNING, no entry stored in dbm for [ENSG00000272779.1] WARNING, no entry stored in dbm for [ENSG00000241288.8] WARNING, no entry stored in dbm for [ENSG00000229723.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000256721.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000227619.3] WARNING, no entry stored in dbm for [ENSG00000227733.10] WARNING, no entry stored in dbm for [ENSG00000243753.5] WARNING, no entry stored in dbm for [ENSG00000181126.13] WARNING, no entry stored in dbm for [ENSG00000233672.9] WARNING, no entry stored in dbm for [ENSG00000281383.1] WARNING, no entry stored in dbm for [ENSG00000262831.1] WARNING, no entry stored in dbm for [ENSG00000280800.1] WARNING, no entry stored in dbm for [ENSG00000262831.1] WARNING, no entry stored in dbm for [ENSG00000281181.1] WARNING, no entry stored in dbm for [ENSG00000262831.1] WARNING, no entry stored in dbm for [ENSG00000280614.1] WARNING, no entry stored in dbm for [ENSG00000262831.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000227627.3] WARNING, no entry stored in dbm for [ENSG00000280997.1] WARNING, no entry stored in dbm for [ENSG00000277287.1] WARNING, no entry stored in dbm for [ENSG00000221953.5] WARNING, no entry stored in dbm for [ENSG00000227195.11] WARNING, no entry stored in dbm for [ENSG00000226548.1] WARNING, no entry stored in dbm for [ENSG00000287400.1] WARNING, no entry stored in dbm for [ENSG00000213871.3] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000230912.1] WARNING, no entry stored in dbm for [ENSG00000203690.13] WARNING, no entry stored in dbm for [ENSG00000279211.1] WARNING, no entry stored in dbm for [ENSG00000255991.2] WARNING, no entry stored in dbm for [ENSG00000213979.3] WARNING, no entry stored in dbm for [ENSG00000250159.7] WARNING, no entry stored in dbm for [ENSG00000224479.6] WARNING, no entry stored in dbm for [ENSG00000254035.1] WARNING, no entry stored in dbm for [ENSG00000247193.3] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000230733.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000259772.6] WARNING, no entry stored in dbm for [ENSG00000270804.1] WARNING, no entry stored in dbm for [ENSG00000257403.2] WARNING, no entry stored in dbm for [ENSG00000189149.12] * STAR-Fusion complete. See output: /tmp/nxf.aD9ZHTmUtE/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)