Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/bd23407f957e59aae9828da014a54f/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz 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/ec/e50ceef7ed8a9ec1ebc85b4ac13ef9/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/e50ceef7ed8a9ec1ebc85b4ac13ef9/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/4de7802266e95e36763fef62c5e2d8/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/bd23407f957e59aae9828da014a54f/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.bowiNehLnx/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.bowiNehLnx/./star-fusion.preliminary -sample contains 9095254 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir -J /tmp/nxf.bowiNehLnx/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.bowiNehLnx/ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=85714.29/min [30000], rate=100000.00/min [40000], rate=88888.89/min [50000], rate=83333.33/min [60000], rate=85714.29/min [70000], rate=89361.70/min [80000], rate=94117.65/min [90000], rate=93103.45/min [100000], rate=89552.24/min [110000], rate=89189.19/min [120000], rate=86746.99/min [130000], rate=87640.45/min [140000], rate=89361.70/min [150000], rate=91836.73/min [160000], rate=94117.65/min [170000], rate=93577.98/min [180000], rate=93913.04/min [190000], rate=94214.88/min [200000], rate=93750.00/min [210000], rate=92647.06/min [220000], rate=90410.96/min [230000], rate=90196.08/min [240000], rate=90566.04/min [250000], rate=89285.71/min [260000], rate=88636.36/min [270000], rate=89502.76/min [280000], rate=90810.81/min [290000], rate=90625.00/min [300000], rate=90000.00/min [310000], rate=89855.07/min [320000], rate=90566.04/min [330000], rate=91666.67/min -building interval tree based on /tmp/nxf.bowiNehLnx/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=85714.29/min [30000], rate=94736.84/min [40000], rate=104347.83/min [50000], rate=100000.00/min [60000], rate=105882.35/min [70000], rate=107692.31/min [80000], rate=109090.91/min [90000], rate=112500.00/min [100000], rate=115384.62/min [110000], rate=115789.47/min [120000], rate=116129.03/min [130000], rate=116417.91/min [140000], rate=116666.67/min [150000], rate=118421.05/min [160000], rate=121518.99/min [170000], rate=121428.57/min [180000], rate=117391.30/min [190000], rate=116326.53/min [200000], rate=117647.06/min [210000], rate=117757.01/min [220000], rate=115789.47/min [230000], rate=114049.59/min [240000], rate=108270.68/min [250000], rate=102739.73/min [260000], rate=99363.06/min [270000], rate=97005.99/min [280000], rate=95454.55/min [290000], rate=95604.40/min [300000], rate=94736.84/min [310000], rate=93939.39/min [320000], rate=93203.88/min [330000], rate=93396.23/min [340000], rate=91891.89/min -building interval tree based on /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=150000.00/min [20000], rate=133333.33/min [30000], rate=163636.36/min [40000], rate=171428.57/min [50000], rate=166666.67/min [60000], rate=163636.36/min [70000], rate=168000.00/min [80000], rate=171428.57/min [90000], rate=163636.36/min [100000], rate=162162.16/min [110000], rate=165000.00/min [120000], rate=167441.86/min [130000], rate=165957.45/min [140000], rate=164705.88/min [150000], rate=166666.67/min [160000], rate=162711.86/min [170000], rate=137837.84/min [180000], rate=124137.93/min [190000], rate=115151.52/min [200000], rate=108108.11/min [210000], rate=102439.02/min [220000], rate=99248.12/min [230000], rate=97872.34/min [240000], rate=96644.30/min [250000], rate=94936.71/min [260000], rate=93975.90/min [270000], rate=94736.84/min [280000], rate=91304.35/min [290000], rate=87437.19/min [300000], rate=85308.06/min [310000], rate=84162.90/min [320000], rate=82758.62/min [330000], rate=82157.68/min -building interval tree based on /tmp/nxf.bowiNehLnx/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=69230.77/min [40000], rate=75000.00/min [50000], rate=78947.37/min [60000], rate=85714.29/min [70000], rate=85714.29/min [80000], rate=88888.89/min [90000], rate=91525.42/min [100000], rate=98360.66/min [110000], rate=98507.46/min [120000], rate=98630.14/min [130000], rate=98734.18/min [140000], rate=100000.00/min [150000], rate=96774.19/min [160000], rate=93203.88/min [170000], rate=90265.49/min [180000], rate=88524.59/min [190000], rate=88372.09/min [200000], rate=83916.08/min [210000], rate=80254.78/min [220000], rate=78571.43/min [230000], rate=77528.09/min [240000], rate=78260.87/min [250000], rate=79365.08/min [260000], rate=79187.82/min [270000], rate=76777.25/min [280000], rate=75675.68/min [290000], rate=75324.68/min [300000], rate=75313.81/min [310000], rate=74400.00/min [320000], rate=72727.27/min [330000], rate=71739.13/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir --filt_file /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.bowiNehLnx/./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... 6000000.00 reads per min processed... 5000000.00 reads per min processed... 5142857.14 reads per min processed... 5250000.00 reads per min processed... 5333333.33 reads per min processed... 5400000.00 reads per min processed... 5000000.00 reads per min processed... 5076923.08 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.bowiNehLnx/ColoN_FFPE_L03_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.bowiNehLnx/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -21728.243281 EM: Round [1] log likelihood: -21663.712832 EM: Round [2] log likelihood: -21636.257725 EM: Round [3] log likelihood: -21622.321145 EM: Round [4] log likelihood: -21614.647840 EM: Round [5] log likelihood: -21610.249488 EM: Round [6] log likelihood: -21607.649787 EM: Round [7] log likelihood: -21606.064707 EM: Round [8] log likelihood: -21605.067046 EM: Round [9] log likelihood: -21604.419437 EM: Round [10] log likelihood: -21603.986695 EM: Round [11] log likelihood: -21603.689623 EM: Round [12] log likelihood: -21603.480497 EM: Round [13] log likelihood: -21603.329785 EM: Round [14] log likelihood: -21603.218760 EM: Round [15] log likelihood: -21603.135273 EM: Round [16] log likelihood: -21603.071273 EM: Round [17] log likelihood: -21603.021314 EM: Round [18] log likelihood: -21602.981646 EM: Round [19] log likelihood: -21602.949642 EM: Round [20] log likelihood: -21602.923431 EM: Round [21] log likelihood: -21602.901659 EM: Round [22] log likelihood: -21602.883335 EM: Round [23] log likelihood: -21602.867726 EM: Round [24] log likelihood: -21602.854279 EM: Round [25] log likelihood: -21602.842574 EM: Round [26] log likelihood: -21602.832290 EM: Round [27] log likelihood: -21602.823177 EM: Round [28] log likelihood: -21602.815039 EM: Round [29] log likelihood: -21602.807721 EM: Round [30] log likelihood: -21602.801100 EM: Round [31] log likelihood: -21602.795077 EM: Round [32] log likelihood: -21602.789570 EM: Round [33] log likelihood: -21602.784513 EM: Round [34] log likelihood: -21602.779852 EM: Round [35] log likelihood: -21602.775540 EM: Round [36] log likelihood: -21602.771538 EM: Round [37] log likelihood: -21602.767815 EM: Round [38] log likelihood: -21602.764343 EM: Round [39] log likelihood: -21602.761097 EM: Round [40] log likelihood: -21602.758056 EM: Round [41] log likelihood: -21602.755204 EM: Round [42] log likelihood: -21602.752523 EM: Round [43] log likelihood: -21602.749999 EM: Round [44] log likelihood: -21602.747621 EM: Round [45] log likelihood: -21602.745377 EM: Round [46] log likelihood: -21602.743258 EM: Round [47] log likelihood: -21602.741253 EM: Round [48] log likelihood: -21602.739355 EM: Round [49] log likelihood: -21602.737556 EM: Round [50] log likelihood: -21602.735851 EM: Round [51] log likelihood: -21602.734232 EM: Round [52] log likelihood: -21602.732694 EM: Round [53] log likelihood: -21602.731232 EM: Round [54] log likelihood: -21602.729840 EM: Round [55] log likelihood: -21602.728516 EM: Round [56] log likelihood: -21602.727254 EM: Round [57] log likelihood: -21602.726050 EM: Round [58] log likelihood: -21602.724902 EM: Round [59] log likelihood: -21602.723806 EM: Round [60] log likelihood: -21602.722759 EM: Round [61] log likelihood: -21602.721759 EM: Round [62] log likelihood: -21602.720802 EM: Round [63] log likelihood: -21602.719886 EM: Round [64] log likelihood: -21602.719009 EM: Round [65] log likelihood: -21602.718170 EM: Round [66] log likelihood: -21602.717365 EM: Round [67] log likelihood: -21602.716593 EM: Round [68] log likelihood: -21602.715853 EM: Round [69] log likelihood: -21602.715143 EM: Round [70] log likelihood: -21602.714461 EM: Round [71] log likelihood: -21602.713805 EM: Round [72] log likelihood: -21602.713176 EM: Round [73] log likelihood: -21602.712570 EM: Round [74] log likelihood: -21602.711988 EM: Round [75] log likelihood: -21602.711428 EM: Round [76] log likelihood: -21602.710889 EM: Round [77] log likelihood: -21602.710370 EM: Round [78] log likelihood: -21602.709870 EM: Round [79] log likelihood: -21602.709389 EM: Round [80] log likelihood: -21602.708925 EM: Round [81] log likelihood: -21602.708478 EM: Round [82] log likelihood: -21602.708047 EM: Round [83] log likelihood: -21602.707631 EM: Round [84] log likelihood: -21602.707230 EM: Round [85] log likelihood: -21602.706843 EM: Round [86] log likelihood: -21602.706470 EM: Round [87] log likelihood: -21602.706109 EM: Round [88] log likelihood: -21602.705761 EM: Round [89] log likelihood: -21602.705425 EM: Round [90] log likelihood: -21602.705100 EM: Round [91] log likelihood: -21602.704787 EM: Round [92] log likelihood: -21602.704484 EM: Round [93] log likelihood: -21602.704191 EM: Round [94] log likelihood: -21602.703908 EM: Round [95] log likelihood: -21602.703634 EM: Round [96] log likelihood: -21602.703370 EM: Round [97] log likelihood: -21602.703114 EM: Round [98] log likelihood: -21602.702867 EM: Round [99] log likelihood: -21602.702628 EM: Round [100] log likelihood: -21602.702396 EM: Round [101] log likelihood: -21602.702173 EM: Round [102] log likelihood: -21602.701956 EM: Round [103] log likelihood: -21602.701747 EM: Round [104] log likelihood: -21602.701544 EM: Round [105] log likelihood: -21602.701348 EM: Round [106] log likelihood: -21602.701158 EM: Round [107] log likelihood: -21602.700974 EM: Round [108] log likelihood: -21602.700796 EM: Round [109] log likelihood: -21602.700624 EM: Round [110] log likelihood: -21602.700457 EM: Round [111] log likelihood: -21602.700296 EM: Round [112] log likelihood: -21602.700140 EM: Round [113] log likelihood: -21602.699988 EM: Round [114] log likelihood: -21602.699842 EM: Round [115] log likelihood: -21602.699700 EM: Round [116] log likelihood: -21602.699562 EM: Round [117] log likelihood: -21602.699429 EM: Round [118] log likelihood: -21602.699300 EM: Round [119] log likelihood: -21602.699175 EM: Round [120] log likelihood: -21602.699054 EM: Round [121] log likelihood: -21602.698936 EM: Round [122] log likelihood: -21602.698822 EM: Round [123] log likelihood: -21602.698712 EM: Round [124] log likelihood: -21602.698605 EM: Round [125] log likelihood: -21602.698502 EM: Round [126] log likelihood: -21602.698401 EM: Round [127] log likelihood: -21602.698304 EM: Stopping iterations at round 127 due to insufficient improvement in likelihood. EM: Starting log likelihood: -21708.793701 EM: Round [1] log likelihood: -21651.949833 EM: Round [2] log likelihood: -21629.000455 EM: Round [3] log likelihood: -21617.745881 EM: Round [4] log likelihood: -21611.692083 EM: Round [5] log likelihood: -21608.283091 EM: Round [6] log likelihood: -21606.299035 EM: Round [7] log likelihood: -21605.106278 EM: Round [8] log likelihood: -21604.365261 EM: Round [9] log likelihood: -21603.890054 EM: Round [10] log likelihood: -21603.576161 EM: Round [11] log likelihood: -21603.363085 EM: Round [12] log likelihood: -21603.214746 EM: Round [13] log likelihood: -21603.109028 EM: Round [14] log likelihood: -21603.032028 EM: Round [15] log likelihood: -21602.974795 EM: Round [16] log likelihood: -21602.931445 EM: Round [17] log likelihood: -21602.898025 EM: Round [18] log likelihood: -21602.871831 EM: Round [19] log likelihood: -21602.850980 EM: Round [20] log likelihood: -21602.834139 EM: Round [21] log likelihood: -21602.820348 EM: Round [22] log likelihood: -21602.808909 EM: Round [23] log likelihood: -21602.799306 EM: Round [24] log likelihood: -21602.791151 EM: Round [25] log likelihood: -21602.784153 EM: Round [26] log likelihood: -21602.778087 EM: Round [27] log likelihood: -21602.772781 EM: Round [28] log likelihood: -21602.768099 EM: Round [29] log likelihood: -21602.763935 EM: Round [30] log likelihood: -21602.760205 EM: Round [31] log likelihood: -21602.756840 EM: Round [32] log likelihood: -21602.753786 EM: Round [33] log likelihood: -21602.750998 EM: Round [34] log likelihood: -21602.748440 EM: Round [35] log likelihood: -21602.746082 EM: Round [36] log likelihood: -21602.743898 EM: Round [37] log likelihood: -21602.741867 EM: Round [38] log likelihood: -21602.739972 EM: Round [39] log likelihood: -21602.738199 EM: Round [40] log likelihood: -21602.736533 EM: Round [41] log likelihood: -21602.734965 EM: Round [42] log likelihood: -21602.733486 EM: Round [43] log likelihood: -21602.732086 EM: Round [44] log likelihood: -21602.730759 EM: Round [45] log likelihood: -21602.729499 EM: Round [46] log likelihood: -21602.728300 EM: Round [47] log likelihood: -21602.727158 EM: Round [48] log likelihood: -21602.726068 EM: Round [49] log likelihood: -21602.725027 EM: Round [50] log likelihood: -21602.724031 EM: Round [51] log likelihood: -21602.723077 EM: Round [52] log likelihood: -21602.722162 EM: Round [53] log likelihood: -21602.721284 EM: Round [54] log likelihood: -21602.720441 EM: Round [55] log likelihood: -21602.719631 EM: Round [56] log likelihood: -21602.718851 EM: Round [57] log likelihood: -21602.718101 EM: Round [58] log likelihood: -21602.717378 EM: Round [59] log likelihood: -21602.716681 EM: Round [60] log likelihood: -21602.716009 EM: Round [61] log likelihood: -21602.715361 EM: Round [62] log likelihood: -21602.714735 EM: Round [63] log likelihood: -21602.714130 EM: Round [64] log likelihood: -21602.713546 EM: Round [65] log likelihood: -21602.712981 EM: Round [66] log likelihood: -21602.712435 EM: Round [67] log likelihood: -21602.711906 EM: Round [68] log likelihood: -21602.711395 EM: Round [69] log likelihood: -21602.710900 EM: Round [70] log likelihood: -21602.710421 EM: Round [71] log likelihood: -21602.709957 EM: Round [72] log likelihood: -21602.709508 EM: Round [73] log likelihood: -21602.709072 EM: Round [74] log likelihood: -21602.708651 EM: Round [75] log likelihood: -21602.708242 EM: Round [76] log likelihood: -21602.707846 EM: Round [77] log likelihood: -21602.707461 EM: Round [78] log likelihood: -21602.707089 EM: Round [79] log likelihood: -21602.706728 EM: Round [80] log likelihood: -21602.706378 EM: Round [81] log likelihood: -21602.706038 EM: Round [82] log likelihood: -21602.705709 EM: Round [83] log likelihood: -21602.705390 EM: Round [84] log likelihood: -21602.705080 EM: Round [85] log likelihood: -21602.704779 EM: Round [86] log likelihood: -21602.704488 EM: Round [87] log likelihood: -21602.704205 EM: Round [88] log likelihood: -21602.703931 EM: Round [89] log likelihood: -21602.703664 EM: Round [90] log likelihood: -21602.703406 EM: Round [91] log likelihood: -21602.703156 EM: Round [92] log likelihood: -21602.702913 EM: Round [93] log likelihood: -21602.702677 EM: Round [94] log likelihood: -21602.702448 EM: Round [95] log likelihood: -21602.702226 EM: Round [96] log likelihood: -21602.702011 EM: Round [97] log likelihood: -21602.701802 EM: Round [98] log likelihood: -21602.701599 EM: Round [99] log likelihood: -21602.701403 EM: Round [100] log likelihood: -21602.701212 EM: Round [101] log likelihood: -21602.701027 EM: Round [102] log likelihood: -21602.700847 EM: Round [103] log likelihood: -21602.700673 EM: Round [104] log likelihood: -21602.700504 EM: Round [105] log likelihood: -21602.700340 EM: Round [106] log likelihood: -21602.700181 EM: Round [107] log likelihood: -21602.700027 EM: Round [108] log likelihood: -21602.699878 EM: Round [109] log likelihood: -21602.699733 EM: Round [110] log likelihood: -21602.699592 EM: Round [111] log likelihood: -21602.699455 EM: Round [112] log likelihood: -21602.699323 EM: Round [113] log likelihood: -21602.699194 EM: Round [114] log likelihood: -21602.699070 EM: Round [115] log likelihood: -21602.698949 EM: Round [116] log likelihood: -21602.698831 EM: Round [117] log likelihood: -21602.698718 EM: Round [118] log likelihood: -21602.698607 EM: Round [119] log likelihood: -21602.698500 EM: Round [120] log likelihood: -21602.698397 EM: Round [121] log likelihood: -21602.698296 EM: Round [122] log likelihood: -21602.698198 EM: Stopping iterations at round 122 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9095254 > /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir > /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir --annotate /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir -done, see /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.bowiNehLnx/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 101, filtered: 1571) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.bowiNehLnx/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.bowiNehLnx/./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.bowiNehLnx/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000267598.1] WARNING, no entry stored in dbm for [ENSG00000229739.4] WARNING, no entry stored in dbm for [ENSG00000251010.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000198555.7] WARNING, no entry stored in dbm for [ENSG00000259945.1] WARNING, no entry stored in dbm for [ENSG00000243352.3] WARNING, no entry stored in dbm for [ENSG00000240116.3] 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 [ENSG00000244230.3] 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 [ENSG00000272068.1] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000287957.1] WARNING, no entry stored in dbm for [ENSG00000231920.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000266053.2] WARNING, no entry stored in dbm for [ENSG00000270799.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000267383.7] WARNING, no entry stored in dbm for [ENSG00000286045.1] 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 [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000255182.2] 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 [ENSG00000181126.13] WARNING, no entry stored in dbm for [ENSG00000227195.11] WARNING, no entry stored in dbm for [ENSG00000270578.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000260464.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000263883.1] 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 [ENSG00000287449.1] WARNING, no entry stored in dbm for [ENSG00000255306.1] WARNING, no entry stored in dbm for [ENSG00000260879.1] WARNING, no entry stored in dbm for [ENSG00000220685.3] WARNING, no entry stored in dbm for [ENSG00000275613.2] WARNING, no entry stored in dbm for [ENSG00000275340.1] WARNING, no entry stored in dbm for [ENSG00000273230.1] WARNING, no entry stored in dbm for [ENSG00000267169.2] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000264044.1] WARNING, no entry stored in dbm for [ENSG00000277283.1] * STAR-Fusion complete. See output: /tmp/nxf.bowiNehLnx/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)