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/71/d0009e84efb333e809cfb15cc5fbcb/EndoN_FFPE_L05_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/7aa3f5a7751cd9cd1f10529cbff77e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/d0009e84efb333e809cfb15cc5fbcb/EndoN_FFPE_L05_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/7aa3f5a7751cd9cd1f10529cbff77e/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/e4f2892bae81f0c3d90764f64bddac/EndoN_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.ROHHqBURqi/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary -sample contains 25491735 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir -J /tmp/nxf.ROHHqBURqi/EndoN_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.ROHHqBURqi/EndoN_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=22222.22/min [20000], rate=21052.63/min [30000], rate=23076.92/min [40000], rate=24742.27/min [50000], rate=25423.73/min [60000], rate=27272.73/min [70000], rate=28965.52/min [80000], rate=30573.25/min [90000], rate=29834.25/min [100000], rate=30303.03/min [110000], rate=32038.83/min [120000], rate=33488.37/min [130000], rate=34361.23/min [140000], rate=35000.00/min [150000], rate=35294.12/min [160000], rate=36363.64/min [170000], rate=36690.65/min [180000], rate=36986.30/min [190000], rate=37133.55/min [200000], rate=37735.85/min [210000], rate=37500.00/min [220000], rate=38372.09/min [230000], rate=38655.46/min [240000], rate=38297.87/min [250000], rate=38461.54/min [260000], rate=38805.97/min [270000], rate=38755.98/min [280000], rate=39252.34/min [290000], rate=39726.03/min [300000], rate=39560.44/min [310000], rate=38993.71/min [320000], rate=39425.05/min [330000], rate=39520.96/min [340000], rate=39688.72/min [350000], rate=40076.34/min [360000], rate=40373.83/min [370000], rate=40659.34/min [380000], rate=40860.22/min [390000], rate=40837.70/min [400000], rate=40133.78/min [410000], rate=38801.26/min [420000], rate=38124.05/min [430000], rate=37068.97/min [440000], rate=36768.80/min [450000], rate=36986.30/min [460000], rate=36997.32/min [470000], rate=37252.31/min [480000], rate=37402.60/min [490000], rate=37595.91/min [500000], rate=37926.68/min [510000], rate=37684.73/min [520000], rate=37681.16/min [530000], rate=38038.28/min [540000], rate=38297.87/min [550000], rate=38641.69/min [560000], rate=38979.12/min -building interval tree based on /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=50000.00/min [30000], rate=42857.14/min [40000], rate=37500.00/min [50000], rate=36585.37/min [60000], rate=38297.87/min [70000], rate=38532.11/min [80000], rate=38400.00/min [90000], rate=40909.09/min [100000], rate=43478.26/min [110000], rate=41250.00/min [120000], rate=38297.87/min [130000], rate=36619.72/min [140000], rate=35897.44/min [150000], rate=35573.12/min [160000], rate=35820.90/min [170000], rate=35416.67/min [180000], rate=35643.56/min [190000], rate=36190.48/min [200000], rate=36474.16/min [210000], rate=36950.15/min [220000], rate=35013.26/min [230000], rate=33990.15/min [240000], rate=33802.82/min [250000], rate=33482.14/min [260000], rate=33121.02/min [270000], rate=33128.83/min [280000], rate=33136.09/min [290000], rate=33461.54/min [300000], rate=33707.87/min [310000], rate=34065.93/min [320000], rate=34657.04/min [330000], rate=34859.15/min [340000], rate=34517.77/min [350000], rate=34201.95/min [360000], rate=34177.22/min [370000], rate=34418.60/min [380000], rate=34703.20/min [390000], rate=34718.10/min [400000], rate=34582.13/min [410000], rate=34647.89/min [420000], rate=34567.90/min [430000], rate=34677.42/min [440000], rate=34736.84/min [450000], rate=35340.31/min [460000], rate=35705.05/min [470000], rate=36107.55/min [480000], rate=36135.51/min [490000], rate=36251.54/min [500000], rate=36319.61/min [510000], rate=36385.26/min [520000], rate=36533.96/min [530000], rate=36805.56/min [540000], rate=37241.38/min [550000], rate=37542.66/min -building interval tree based on /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=54545.45/min [20000], rate=63157.89/min [30000], rate=69230.77/min [40000], rate=70588.24/min [50000], rate=62500.00/min [60000], rate=57142.86/min [70000], rate=60000.00/min [80000], rate=61538.46/min [90000], rate=58064.52/min [100000], rate=55045.87/min [110000], rate=53658.54/min [120000], rate=53333.33/min [130000], rate=53424.66/min [140000], rate=50909.09/min [150000], rate=46391.75/min [160000], rate=47290.64/min [170000], rate=47663.55/min [180000], rate=47161.57/min [190000], rate=47302.90/min [200000], rate=47808.76/min [210000], rate=45652.17/min [220000], rate=43564.36/min [230000], rate=42461.54/min [240000], rate=42228.74/min [250000], rate=41551.25/min [260000], rate=41269.84/min [270000], rate=41116.75/min [280000], rate=40579.71/min [290000], rate=40277.78/min [300000], rate=40358.74/min [310000], rate=40522.88/min [320000], rate=38787.88/min [330000], rate=37858.51/min [340000], rate=37226.28/min [350000], rate=36713.29/min [360000], rate=36302.52/min [370000], rate=35922.33/min [380000], rate=35458.79/min [390000], rate=35454.55/min [400000], rate=35502.96/min [410000], rate=35652.17/min [420000], rate=35846.37/min [430000], rate=36185.13/min [440000], rate=36263.74/min [450000], rate=35856.57/min [460000], rate=34936.71/min [470000], rate=34223.30/min [480000], rate=34042.55/min [490000], rate=33793.10/min [500000], rate=33670.03/min [510000], rate=33812.15/min [520000], rate=34023.99/min [530000], rate=34378.38/min [540000], rate=34801.29/min [550000], rate=34994.70/min -building interval tree based on /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=109090.91/min [30000], rate=128571.43/min [40000], rate=133333.33/min [50000], rate=130434.78/min [60000], rate=116129.03/min [70000], rate=120000.00/min [80000], rate=120000.00/min [90000], rate=103846.15/min [100000], rate=103448.28/min [110000], rate=106451.61/min [120000], rate=107462.69/min [130000], rate=106849.32/min [140000], rate=106329.11/min [150000], rate=108433.73/min [160000], rate=84210.53/min [170000], rate=64556.96/min [180000], rate=48430.49/min [190000], rate=40860.22/min [200000], rate=35294.12/min [210000], rate=32142.86/min [220000], rate=30626.45/min [230000], rate=29550.32/min [240000], rate=28973.84/min [250000], rate=28517.11/min [260000], rate=28312.16/min [270000], rate=28371.28/min [280000], rate=28426.40/min [290000], rate=28855.72/min [300000], rate=29363.78/min [310000], rate=29570.75/min [320000], rate=29402.76/min [330000], rate=29333.33/min [340000], rate=29565.22/min [350000], rate=29957.20/min [360000], rate=30422.54/min [370000], rate=30833.33/min [380000], rate=31448.28/min [390000], rate=31325.30/min [400000], rate=30848.33/min [410000], rate=30711.61/min [420000], rate=30656.93/min [430000], rate=30824.37/min [440000], rate=30949.59/min [450000], rate=31034.48/min [460000], rate=31046.12/min [470000], rate=31194.69/min [480000], rate=31509.85/min [490000], rate=31852.65/min [500000], rate=32292.79/min [510000], rate=32415.25/min [520000], rate=32466.18/min [530000], rate=32682.43/min [540000], rate=32694.25/min [550000], rate=32934.13/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir --filt_file /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.ROHHqBURqi/./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... 3600000.00 reads per min processed... 3428571.43 reads per min processed... 3750000.00 reads per min processed... 3600000.00 reads per min processed... 3230769.23 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3157894.74 reads per min processed... 3142857.14 reads per min processed... 3272727.27 reads per min processed... 3391304.35 reads per min processed... 3360000.00 reads per min processed... 3333333.33 reads per min processed... 3428571.43 reads per min processed... 3290322.58 reads per min processed... 3272727.27 reads per min processed... 3257142.86 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.ROHHqBURqi/EndoN_FFPE_L05_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.ROHHqBURqi/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -33006.626047 EM: Round [1] log likelihood: -32937.309059 EM: Round [2] log likelihood: -32909.054121 EM: Round [3] log likelihood: -32895.183486 EM: Round [4] log likelihood: -32887.749422 EM: Round [5] log likelihood: -32883.560993 EM: Round [6] log likelihood: -32881.096889 EM: Round [7] log likelihood: -32879.579564 EM: Round [8] log likelihood: -32878.600283 EM: Round [9] log likelihood: -32877.939285 EM: Round [10] log likelihood: -32877.474999 EM: Round [11] log likelihood: -32877.137787 EM: Round [12] log likelihood: -32876.886169 EM: Round [13] log likelihood: -32876.694396 EM: Round [14] log likelihood: -32876.545807 EM: Round [15] log likelihood: -32876.429187 EM: Round [16] log likelihood: -32876.336709 EM: Round [17] log likelihood: -32876.262746 EM: Round [18] log likelihood: -32876.203153 EM: Round [19] log likelihood: -32876.154819 EM: Round [20] log likelihood: -32876.115375 EM: Round [21] log likelihood: -32876.082999 EM: Round [22] log likelihood: -32876.056276 EM: Round [23] log likelihood: -32876.034100 EM: Round [24] log likelihood: -32876.015601 EM: Round [25] log likelihood: -32876.000093 EM: Round [26] log likelihood: -32875.987028 EM: Round [27] log likelihood: -32875.975968 EM: Round [28] log likelihood: -32875.966564 EM: Round [29] log likelihood: -32875.958533 EM: Round [30] log likelihood: -32875.951644 EM: Round [31] log likelihood: -32875.945711 EM: Round [32] log likelihood: -32875.940580 EM: Round [33] log likelihood: -32875.936128 EM: Round [34] log likelihood: -32875.932249 EM: Round [35] log likelihood: -32875.928858 EM: Round [36] log likelihood: -32875.925883 EM: Round [37] log likelihood: -32875.923264 EM: Round [38] log likelihood: -32875.920952 EM: Round [39] log likelihood: -32875.918904 EM: Round [40] log likelihood: -32875.917085 EM: Round [41] log likelihood: -32875.915465 EM: Round [42] log likelihood: -32875.914017 EM: Round [43] log likelihood: -32875.912720 EM: Round [44] log likelihood: -32875.911555 EM: Round [45] log likelihood: -32875.910506 EM: Round [46] log likelihood: -32875.909560 EM: Round [47] log likelihood: -32875.908704 EM: Round [48] log likelihood: -32875.907928 EM: Round [49] log likelihood: -32875.907222 EM: Round [50] log likelihood: -32875.906580 EM: Round [51] log likelihood: -32875.905995 EM: Round [52] log likelihood: -32875.905459 EM: Round [53] log likelihood: -32875.904969 EM: Round [54] log likelihood: -32875.904519 EM: Round [55] log likelihood: -32875.904106 EM: Round [56] log likelihood: -32875.903725 EM: Round [57] log likelihood: -32875.903374 EM: Round [58] log likelihood: -32875.903051 EM: Round [59] log likelihood: -32875.902751 EM: Round [60] log likelihood: -32875.902474 EM: Round [61] log likelihood: -32875.902217 EM: Round [62] log likelihood: -32875.901979 EM: Round [63] log likelihood: -32875.901757 EM: Round [64] log likelihood: -32875.901551 EM: Round [65] log likelihood: -32875.901359 EM: Round [66] log likelihood: -32875.901180 EM: Round [67] log likelihood: -32875.901013 EM: Round [68] log likelihood: -32875.900857 EM: Round [69] log likelihood: -32875.900711 EM: Round [70] log likelihood: -32875.900575 EM: Round [71] log likelihood: -32875.900447 EM: Round [72] log likelihood: -32875.900327 EM: Round [73] log likelihood: -32875.900215 EM: Round [74] log likelihood: -32875.900109 EM: Round [75] log likelihood: -32875.900010 EM: Stopping iterations at round 75 due to insufficient improvement in likelihood. EM: Starting log likelihood: -32989.995522 EM: Round [1] log likelihood: -32927.802283 EM: Round [2] log likelihood: -32903.560447 EM: Round [3] log likelihood: -32891.880218 EM: Round [4] log likelihood: -32885.673049 EM: Round [5] log likelihood: -32882.199699 EM: Round [6] log likelihood: -32880.170682 EM: Round [7] log likelihood: -32878.929488 EM: Round [8] log likelihood: -32878.132285 EM: Round [9] log likelihood: -32877.595325 EM: Round [10] log likelihood: -32877.217839 EM: Round [11] log likelihood: -32876.942727 EM: Round [12] log likelihood: -32876.736361 EM: Round [13] log likelihood: -32876.578084 EM: Round [14] log likelihood: -32876.454628 EM: Round [15] log likelihood: -32876.357090 EM: Round [16] log likelihood: -32876.279256 EM: Round [17] log likelihood: -32876.216639 EM: Round [18] log likelihood: -32876.165913 EM: Round [19] log likelihood: -32876.124562 EM: Round [20] log likelihood: -32876.090658 EM: Round [21] log likelihood: -32876.062707 EM: Round [22] log likelihood: -32876.039540 EM: Round [23] log likelihood: -32876.020238 EM: Round [24] log likelihood: -32876.004075 EM: Round [25] log likelihood: -32875.990474 EM: Round [26] log likelihood: -32875.978973 EM: Round [27] log likelihood: -32875.969204 EM: Round [28] log likelihood: -32875.960867 EM: Round [29] log likelihood: -32875.953721 EM: Round [30] log likelihood: -32875.947571 EM: Round [31] log likelihood: -32875.942255 EM: Round [32] log likelihood: -32875.937643 EM: Round [33] log likelihood: -32875.933626 EM: Round [34] log likelihood: -32875.930114 EM: Round [35] log likelihood: -32875.927033 EM: Round [36] log likelihood: -32875.924320 EM: Round [37] log likelihood: -32875.921925 EM: Round [38] log likelihood: -32875.919802 EM: Round [39] log likelihood: -32875.917916 EM: Round [40] log likelihood: -32875.916234 EM: Round [41] log likelihood: -32875.914731 EM: Round [42] log likelihood: -32875.913384 EM: Round [43] log likelihood: -32875.912173 EM: Round [44] log likelihood: -32875.911082 EM: Round [45] log likelihood: -32875.910097 EM: Round [46] log likelihood: -32875.909205 EM: Round [47] log likelihood: -32875.908395 EM: Round [48] log likelihood: -32875.907659 EM: Round [49] log likelihood: -32875.906989 EM: Round [50] log likelihood: -32875.906377 EM: Round [51] log likelihood: -32875.905817 EM: Round [52] log likelihood: -32875.905304 EM: Round [53] log likelihood: -32875.904833 EM: Round [54] log likelihood: -32875.904400 EM: Round [55] log likelihood: -32875.904001 EM: Round [56] log likelihood: -32875.903633 EM: Round [57] log likelihood: -32875.903293 EM: Round [58] log likelihood: -32875.902979 EM: Round [59] log likelihood: -32875.902688 EM: Round [60] log likelihood: -32875.902418 EM: Round [61] log likelihood: -32875.902167 EM: Round [62] log likelihood: -32875.901934 EM: Round [63] log likelihood: -32875.901718 EM: Round [64] log likelihood: -32875.901516 EM: Round [65] log likelihood: -32875.901327 EM: Round [66] log likelihood: -32875.901152 EM: Round [67] log likelihood: -32875.900987 EM: Round [68] log likelihood: -32875.900834 EM: Round [69] log likelihood: -32875.900690 EM: Round [70] log likelihood: -32875.900555 EM: Round [71] log likelihood: -32875.900429 EM: Round [72] log likelihood: -32875.900311 EM: Round [73] log likelihood: -32875.900200 EM: Round [74] log likelihood: -32875.900096 EM: Round [75] log likelihood: -32875.899998 EM: Stopping iterations at round 75 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.ROHHqBURqi/./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.ROHHqBURqi/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.ROHHqBURqi/./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.ROHHqBURqi/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 25491735 > /tmp/nxf.ROHHqBURqi/./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.ROHHqBURqi/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir > /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir --annotate /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.ROHHqBURqi/./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.ROHHqBURqi/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir -done, see /tmp/nxf.ROHHqBURqi/./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.ROHHqBURqi/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.ROHHqBURqi/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 193, filtered: 2732) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.ROHHqBURqi/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.ROHHqBURqi/./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.ROHHqBURqi/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000265735.2] WARNING, no entry stored in dbm for [ENSG00000240116.3] WARNING, no entry stored in dbm for [ENSG00000276168.1] WARNING, no entry stored in dbm for [ENSG00000240116.3] WARNING, no entry stored in dbm for [ENSG00000256195.3] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000245067.7] WARNING, no entry stored in dbm for [ENSG00000214614.3] WARNING, no entry stored in dbm for [ENSG00000239407.5] WARNING, no entry stored in dbm for [ENSG00000223546.7] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000262445.3] WARNING, no entry stored in dbm for [ENSG00000277741.4] WARNING, no entry stored in dbm for [ENSG00000287910.1] WARNING, no entry stored in dbm for [ENSG00000256817.1] WARNING, no entry stored in dbm for [ENSG00000234782.3] WARNING, no entry stored in dbm for [ENSG00000280383.1] WARNING, no entry stored in dbm for [ENSG00000240549.2] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000287243.2] WARNING, no entry stored in dbm for [ENSG00000230071.2] WARNING, no entry stored in dbm for [ENSG00000277739.1] WARNING, no entry stored in dbm for [ENSG00000283568.1] WARNING, no entry stored in dbm for [ENSG00000266433.6] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000213238.6] WARNING, no entry stored in dbm for [ENSG00000205853.12] WARNING, no entry stored in dbm for [ENSG00000239899.3] WARNING, no entry stored in dbm for [ENSG00000276588.1] WARNING, no entry stored in dbm for [ENSG00000239899.3] WARNING, no entry stored in dbm for [ENSG00000277483.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000259540.1] WARNING, no entry stored in dbm for [ENSG00000260698.1] WARNING, no entry stored in dbm for [ENSG00000183239.5] WARNING, no entry stored in dbm for [ENSG00000227195.11] WARNING, no entry stored in dbm for [ENSG00000281128.2] WARNING, no entry stored in dbm for [ENSG00000285786.1] WARNING, no entry stored in dbm for [ENSG00000279266.1] WARNING, no entry stored in dbm for [ENSG00000287738.1] WARNING, no entry stored in dbm for [ENSG00000245532.9] WARNING, no entry stored in dbm for [ENSG00000224116.7] WARNING, no entry stored in dbm for [ENSG00000236753.7] WARNING, no entry stored in dbm for [ENSG00000214548.18] WARNING, no entry stored in dbm for [ENSG00000251562.8] WARNING, no entry stored in dbm for [ENSG00000259663.2] WARNING, no entry stored in dbm for [ENSG00000233058.2] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000260807.7] 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 [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000248441.7] WARNING, no entry stored in dbm for [ENSG00000262585.1] WARNING, no entry stored in dbm for [ENSG00000231528.3] WARNING, no entry stored in dbm for [ENSG00000283103.3] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000231246.2] WARNING, no entry stored in dbm for [ENSG00000279388.1] WARNING, no entry stored in dbm for [ENSG00000224074.3] WARNING, no entry stored in dbm for [ENSG00000228107.1] WARNING, no entry stored in dbm for [ENSG00000259834.1] WARNING, no entry stored in dbm for [ENSG00000274727.1] WARNING, no entry stored in dbm for [ENSG00000236526.1] WARNING, no entry stored in dbm for [ENSG00000272734.1] WARNING, no entry stored in dbm for [ENSG00000224205.2] WARNING, no entry stored in dbm for [ENSG00000278975.1] * STAR-Fusion complete. See output: /tmp/nxf.ROHHqBURqi/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)