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/79/71117a58f0b32aa82ed8ea882f6136/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/847cf9946eb07c11015704a9f80e5a/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/d87f91e10b50ed84d0fdcfa8ac8a5f/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/d87f91e10b50ed84d0fdcfa8ac8a5f/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/847cf9946eb07c11015704a9f80e5a/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.h2FlaRn7Dp/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary -sample contains 33125823 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir -J /tmp/nxf.h2FlaRn7Dp/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.h2FlaRn7Dp/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=50000.00/min [20000], rate=50000.00/min [30000], rate=56250.00/min [40000], rate=53333.33/min [50000], rate=41095.89/min [60000], rate=38297.87/min [70000], rate=37500.00/min [80000], rate=37209.30/min [90000], rate=38297.87/min [100000], rate=38961.04/min [110000], rate=39520.96/min [120000], rate=40909.09/min [130000], rate=41935.48/min [140000], rate=42857.14/min [150000], rate=43689.32/min [160000], rate=44859.81/min [170000], rate=46153.85/min [180000], rate=46551.72/min [190000], rate=46913.58/min [200000], rate=48583.00/min [210000], rate=49802.37/min [220000], rate=50190.11/min [230000], rate=49462.37/min [240000], rate=49655.17/min [250000], rate=49668.87/min [260000], rate=50649.35/min [270000], rate=50625.00/min [280000], rate=51376.15/min [290000], rate=53048.78/min [300000], rate=54216.87/min [310000], rate=53913.04/min [320000], rate=53333.33/min [330000], rate=51968.50/min [340000], rate=52442.16/min [350000], rate=51980.20/min [360000], rate=52173.91/min [370000], rate=51869.16/min [380000], rate=50442.48/min [390000], rate=50980.39/min [400000], rate=50209.21/min [410000], rate=49797.57/min [420000], rate=49704.14/min [430000], rate=50097.09/min [440000], rate=50965.25/min [450000], rate=51823.42/min [460000], rate=52272.73/min [470000], rate=52416.36/min [480000], rate=51705.57/min [490000], rate=51943.46/min [500000], rate=52173.91/min [510000], rate=52040.82/min [520000], rate=52881.36/min [530000], rate=53716.22/min [540000], rate=53731.34/min [550000], rate=53054.66/min [560000], rate=53248.81/min [570000], rate=53773.58/min [580000], rate=54121.31/min [590000], rate=54461.54/min [600000], rate=54711.25/min [610000], rate=55203.62/min [620000], rate=55522.39/min [630000], rate=55834.56/min [640000], rate=56140.35/min [650000], rate=55954.09/min [660000], rate=56090.65/min [670000], rate=55678.67/min [680000], rate=55359.57/min [690000], rate=55053.19/min [700000], rate=55118.11/min [710000], rate=54406.13/min [720000], rate=53399.26/min [730000], rate=52834.74/min [740000], rate=52235.29/min [750000], rate=51369.86/min -building interval tree based on /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=120000.00/min [20000], rate=109090.91/min [30000], rate=150000.00/min [40000], rate=141176.47/min [50000], rate=136363.64/min [60000], rate=133333.33/min [70000], rate=140000.00/min [80000], rate=145454.55/min [90000], rate=142105.26/min [100000], rate=142857.14/min [110000], rate=157142.86/min [120000], rate=167441.86/min [130000], rate=162500.00/min [140000], rate=155555.56/min [150000], rate=163636.36/min [160000], rate=160000.00/min [170000], rate=156923.08/min [180000], rate=154285.71/min [190000], rate=154054.05/min [200000], rate=153846.15/min [210000], rate=151807.23/min [220000], rate=153488.37/min [230000], rate=160465.12/min [240000], rate=165517.24/min [250000], rate=163043.48/min [260000], rate=160824.74/min [270000], rate=162000.00/min [280000], rate=163106.80/min [290000], rate=156756.76/min [300000], rate=147540.98/min [310000], rate=145312.50/min [320000], rate=145454.55/min [330000], rate=145588.24/min [340000], rate=145714.29/min [350000], rate=144827.59/min [360000], rate=144966.44/min [370000], rate=144155.84/min [380000], rate=145222.93/min [390000], rate=145341.61/min [400000], rate=144578.31/min [410000], rate=141379.31/min [420000], rate=142372.88/min [430000], rate=142541.44/min [440000], rate=142702.70/min [450000], rate=132352.94/min [460000], rate=106153.85/min [470000], rate=88401.25/min [480000], rate=77837.84/min [490000], rate=71707.32/min [500000], rate=65789.47/min [510000], rate=60714.29/min [520000], rate=57142.86/min [530000], rate=54922.28/min [540000], rate=53820.60/min [550000], rate=52800.00/min [560000], rate=51612.90/min [570000], rate=50892.86/min [580000], rate=50877.19/min [590000], rate=51082.25/min [600000], rate=51136.36/min [610000], rate=51046.03/min [620000], rate=50958.90/min [630000], rate=50670.24/min [640000], rate=50526.32/min [650000], rate=50649.35/min [660000], rate=50574.71/min [670000], rate=50693.57/min [680000], rate=50308.26/min [690000], rate=50303.77/min [700000], rate=50420.17/min [710000], rate=50473.93/min [720000], rate=49146.76/min [730000], rate=48720.80/min [740000], rate=48156.18/min [750000], rate=47720.04/min -building interval tree based on /tmp/nxf.h2FlaRn7Dp/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=63157.89/min [30000], rate=56250.00/min [40000], rate=63157.89/min [50000], rate=60000.00/min [60000], rate=61016.95/min [70000], rate=64615.38/min [80000], rate=60000.00/min [90000], rate=58064.52/min [100000], rate=59405.94/min [110000], rate=58407.08/min [120000], rate=59016.39/min [130000], rate=59541.98/min [140000], rate=60000.00/min [150000], rate=61224.49/min [160000], rate=59259.26/min [170000], rate=56043.96/min [180000], rate=53465.35/min [190000], rate=53023.26/min [200000], rate=52173.91/min [210000], rate=51428.57/min [220000], rate=50965.25/min [230000], rate=50000.00/min [240000], rate=50000.00/min [250000], rate=49668.87/min [260000], rate=47272.73/min [270000], rate=45633.80/min [280000], rate=43636.36/min [290000], rate=43283.58/min [300000], rate=42553.19/min [310000], rate=42465.75/min [320000], rate=43049.33/min [330000], rate=43902.44/min [340000], rate=44347.83/min [350000], rate=44491.53/min [360000], rate=44536.08/min [370000], rate=43786.98/min [380000], rate=42379.18/min [390000], rate=41489.36/min [400000], rate=40816.33/min [410000], rate=40863.79/min [420000], rate=40710.82/min [430000], rate=40375.59/min [440000], rate=40366.97/min [450000], rate=40601.50/min [460000], rate=40949.55/min [470000], rate=40928.88/min [480000], rate=41142.86/min [490000], rate=41004.18/min [500000], rate=40705.56/min [510000], rate=40316.21/min [520000], rate=40258.06/min [530000], rate=40304.18/min [540000], rate=40449.44/min [550000], rate=40791.10/min [560000], rate=41126.07/min [570000], rate=41204.82/min [580000], rate=41232.23/min [590000], rate=41162.79/min [600000], rate=41189.93/min [610000], rate=41169.85/min [620000], rate=41425.39/min [630000], rate=41767.96/min [640000], rate=42151.48/min [650000], rate=42299.35/min [660000], rate=42580.65/min [670000], rate=42675.16/min [680000], rate=42722.51/min [690000], rate=42724.46/min [700000], rate=42813.46/min [710000], rate=42900.30/min [720000], rate=43286.57/min [730000], rate=43538.77/min [740000], rate=44003.96/min [750000], rate=44334.98/min -building interval tree based on /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=50000.00/min [20000], rate=48000.00/min [30000], rate=46153.85/min [40000], rate=43636.36/min [50000], rate=42857.14/min [60000], rate=45569.62/min [70000], rate=48275.86/min [80000], rate=50526.32/min [90000], rate=52941.18/min [100000], rate=48387.10/min [110000], rate=46478.87/min [120000], rate=45569.62/min [130000], rate=45086.71/min [140000], rate=42639.59/min [150000], rate=41666.67/min [160000], rate=42666.67/min [170000], rate=43776.82/min [180000], rate=45188.28/min [190000], rate=46530.61/min [200000], rate=47244.09/min [210000], rate=47727.27/min [220000], rate=48000.00/min [230000], rate=48421.05/min [240000], rate=47840.53/min [250000], rate=46728.97/min [260000], rate=46290.80/min [270000], rate=45892.35/min [280000], rate=46153.85/min [290000], rate=46276.60/min [300000], rate=46035.81/min [310000], rate=45700.25/min [320000], rate=46043.17/min [330000], rate=46046.51/min [340000], rate=45842.70/min [350000], rate=46255.51/min [360000], rate=46551.72/min [370000], rate=46443.51/min [380000], rate=44618.40/min [390000], rate=44656.49/min [400000], rate=43795.62/min [410000], rate=43309.86/min [420000], rate=43003.41/min [430000], rate=42574.26/min [440000], rate=42307.69/min [450000], rate=42121.68/min [460000], rate=41503.76/min [470000], rate=41409.69/min [480000], rate=41739.13/min [490000], rate=42060.09/min [500000], rate=42372.88/min [510000], rate=41860.47/min [520000], rate=40677.97/min [530000], rate=40151.52/min [540000], rate=39754.60/min [550000], rate=39807.00/min [560000], rate=39857.65/min [570000], rate=39767.44/min [580000], rate=39277.65/min [590000], rate=38646.29/min [600000], rate=38668.10/min [610000], rate=38894.79/min [620000], rate=39157.89/min [630000], rate=39334.03/min [640000], rate=39384.62/min [650000], rate=39836.57/min [660000], rate=40203.05/min [670000], rate=40565.09/min [680000], rate=40197.04/min [690000], rate=39884.39/min [700000], rate=39961.94/min [710000], rate=39962.48/min [720000], rate=40037.07/min [730000], rate=39854.41/min [740000], rate=39678.28/min [750000], rate=39893.62/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir --filt_file /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 0.00 reads per min processed... 12000000.00 reads per min processed... 18000000.00 reads per min processed... 12000000.00 reads per min processed... 7500000.00 reads per min processed... 5142857.14 reads per min processed... 4666666.67 reads per min processed... 4363636.36 reads per min processed... 4153846.15 reads per min processed... 3750000.00 reads per min processed... 3473684.21 reads per min processed... 3428571.43 reads per min processed... 3391304.35 reads per min processed... 3360000.00 reads per min processed... 3461538.46 reads per min processed... 3428571.43 reads per min processed... 3642857.14 reads per min processed... 3724137.93 reads per min processed... 3677419.35 reads per min processed... 3636363.64 reads per min processed... 3600000.00 reads per min processed... 3567567.57 reads per min processed... 3538461.54 reads per min processed... 3428571.43 reads per min processed... 3409090.91 reads per min processed... 3391304.35 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.h2FlaRn7Dp/BreastNP_FFPE_L04_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.h2FlaRn7Dp/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -40075.991721 EM: Round [1] log likelihood: -39986.308720 EM: Round [2] log likelihood: -39948.816065 EM: Round [3] log likelihood: -39930.100910 EM: Round [4] log likelihood: -39919.884110 EM: Round [5] log likelihood: -39914.041051 EM: Round [6] log likelihood: -39910.575486 EM: Round [7] log likelihood: -39908.444311 EM: Round [8] log likelihood: -39907.085844 EM: Round [9] log likelihood: -39906.190140 EM: Round [10] log likelihood: -39905.581190 EM: Round [11] log likelihood: -39905.155814 EM: Round [12] log likelihood: -39904.851535 EM: Round [13] log likelihood: -39904.629325 EM: Round [14] log likelihood: -39904.464085 EM: Round [15] log likelihood: -39904.339245 EM: Round [16] log likelihood: -39904.243599 EM: Round [17] log likelihood: -39904.169405 EM: Round [18] log likelihood: -39904.111210 EM: Round [19] log likelihood: -39904.065110 EM: Round [20] log likelihood: -39904.028262 EM: Round [21] log likelihood: -39903.998570 EM: Round [22] log likelihood: -39903.974466 EM: Round [23] log likelihood: -39903.954768 EM: Round [24] log likelihood: -39903.938568 EM: Round [25] log likelihood: -39903.925170 EM: Round [26] log likelihood: -39903.914029 EM: Round [27] log likelihood: -39903.904720 EM: Round [28] log likelihood: -39903.896903 EM: Round [29] log likelihood: -39903.890312 EM: Round [30] log likelihood: -39903.884729 EM: Round [31] log likelihood: -39903.879982 EM: Round [32] log likelihood: -39903.875929 EM: Round [33] log likelihood: -39903.872456 EM: Round [34] log likelihood: -39903.869468 EM: Round [35] log likelihood: -39903.866889 EM: Round [36] log likelihood: -39903.864654 EM: Round [37] log likelihood: -39903.862711 EM: Round [38] log likelihood: -39903.861015 EM: Round [39] log likelihood: -39903.859531 EM: Round [40] log likelihood: -39903.858227 EM: Round [41] log likelihood: -39903.857077 EM: Round [42] log likelihood: -39903.856061 EM: Round [43] log likelihood: -39903.855159 EM: Round [44] log likelihood: -39903.854355 EM: Round [45] log likelihood: -39903.853638 EM: Round [46] log likelihood: -39903.852995 EM: Round [47] log likelihood: -39903.852418 EM: Round [48] log likelihood: -39903.851897 EM: Round [49] log likelihood: -39903.851426 EM: Round [50] log likelihood: -39903.850998 EM: Round [51] log likelihood: -39903.850610 EM: Round [52] log likelihood: -39903.850256 EM: Round [53] log likelihood: -39903.849931 EM: Round [54] log likelihood: -39903.849634 EM: Round [55] log likelihood: -39903.849361 EM: Round [56] log likelihood: -39903.849109 EM: Round [57] log likelihood: -39903.848877 EM: Round [58] log likelihood: -39903.848662 EM: Round [59] log likelihood: -39903.848462 EM: Round [60] log likelihood: -39903.848276 EM: Round [61] log likelihood: -39903.848103 EM: Round [62] log likelihood: -39903.847942 EM: Round [63] log likelihood: -39903.847791 EM: Round [64] log likelihood: -39903.847650 EM: Round [65] log likelihood: -39903.847517 EM: Round [66] log likelihood: -39903.847393 EM: Round [67] log likelihood: -39903.847276 EM: Round [68] log likelihood: -39903.847166 EM: Round [69] log likelihood: -39903.847062 EM: Round [70] log likelihood: -39903.846964 EM: Stopping iterations at round 70 due to insufficient improvement in likelihood. EM: Starting log likelihood: -40058.028998 EM: Round [1] log likelihood: -39975.770282 EM: Round [2] log likelihood: -39942.342874 EM: Round [3] log likelihood: -39926.029848 EM: Round [4] log likelihood: -39917.271612 EM: Round [5] log likelihood: -39912.323410 EM: Round [6] log likelihood: -39909.414764 EM: Round [7] log likelihood: -39907.637914 EM: Round [8] log likelihood: -39906.510882 EM: Round [9] log likelihood: -39905.770461 EM: Round [10] log likelihood: -39905.268383 EM: Round [11] log likelihood: -39904.918290 EM: Round [12] log likelihood: -39904.668169 EM: Round [13] log likelihood: -39904.485666 EM: Round [14] log likelihood: -39904.350045 EM: Round [15] log likelihood: -39904.247647 EM: Round [16] log likelihood: -39904.169248 EM: Round [17] log likelihood: -39904.108481 EM: Round [18] log likelihood: -39904.060865 EM: Round [19] log likelihood: -39904.023188 EM: Round [20] log likelihood: -39903.993113 EM: Round [21] log likelihood: -39903.968915 EM: Round [22] log likelihood: -39903.949305 EM: Round [23] log likelihood: -39903.933306 EM: Round [24] log likelihood: -39903.920175 EM: Round [25] log likelihood: -39903.909335 EM: Round [26] log likelihood: -39903.900340 EM: Round [27] log likelihood: -39903.892839 EM: Round [28] log likelihood: -39903.886553 EM: Round [29] log likelihood: -39903.881263 EM: Round [30] log likelihood: -39903.876791 EM: Round [31] log likelihood: -39903.872995 EM: Round [32] log likelihood: -39903.869760 EM: Round [33] log likelihood: -39903.866991 EM: Round [34] log likelihood: -39903.864613 EM: Round [35] log likelihood: -39903.862562 EM: Round [36] log likelihood: -39903.860787 EM: Round [37] log likelihood: -39903.859245 EM: Round [38] log likelihood: -39903.857900 EM: Round [39] log likelihood: -39903.856722 EM: Round [40] log likelihood: -39903.855688 EM: Round [41] log likelihood: -39903.854775 EM: Round [42] log likelihood: -39903.853968 EM: Round [43] log likelihood: -39903.853251 EM: Round [44] log likelihood: -39903.852611 EM: Round [45] log likelihood: -39903.852039 EM: Round [46] log likelihood: -39903.851526 EM: Round [47] log likelihood: -39903.851063 EM: Round [48] log likelihood: -39903.850646 EM: Round [49] log likelihood: -39903.850267 EM: Round [50] log likelihood: -39903.849922 EM: Round [51] log likelihood: -39903.849608 EM: Round [52] log likelihood: -39903.849321 EM: Round [53] log likelihood: -39903.849057 EM: Round [54] log likelihood: -39903.848814 EM: Round [55] log likelihood: -39903.848590 EM: Round [56] log likelihood: -39903.848383 EM: Round [57] log likelihood: -39903.848191 EM: Round [58] log likelihood: -39903.848013 EM: Round [59] log likelihood: -39903.847847 EM: Round [60] log likelihood: -39903.847693 EM: Round [61] log likelihood: -39903.847548 EM: Round [62] log likelihood: -39903.847413 EM: Round [63] log likelihood: -39903.847286 EM: Round [64] log likelihood: -39903.847166 EM: Round [65] log likelihood: -39903.847054 EM: Round [66] log likelihood: -39903.846949 EM: Round [67] log likelihood: -39903.846849 EM: Stopping iterations at round 67 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.h2FlaRn7Dp/./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.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.h2FlaRn7Dp/./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.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 33125823 > /tmp/nxf.h2FlaRn7Dp/./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.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir > /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir --annotate /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.h2FlaRn7Dp/./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.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir -done, see /tmp/nxf.h2FlaRn7Dp/./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.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.h2FlaRn7Dp/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 260, filtered: 2906) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.h2FlaRn7Dp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.h2FlaRn7Dp/./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.h2FlaRn7Dp/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000128438.10] WARNING, no entry stored in dbm for [ENSG00000223202.1] WARNING, no entry stored in dbm for [ENSG00000200966.1] WARNING, no entry stored in dbm for [ENSG00000172460.17] WARNING, no entry stored in dbm for [ENSG00000272235.1] WARNING, no entry stored in dbm for [ENSG00000217896.2] WARNING, no entry stored in dbm for [ENSG00000231064.7] WARNING, no entry stored in dbm for [ENSG00000207652.1] WARNING, no entry stored in dbm for [ENSG00000207652.1] WARNING, no entry stored in dbm for [ENSG00000207652.1] WARNING, no entry stored in dbm for [ENSG00000207652.1] WARNING, no entry stored in dbm for [ENSG00000207652.1] WARNING, no entry stored in dbm for [ENSG00000207652.1] WARNING, no entry stored in dbm for [ENSG00000207652.1] WARNING, no entry stored in dbm for [ENSG00000207652.1] WARNING, no entry stored in dbm for [ENSG00000227954.7] WARNING, no entry stored in dbm for [ENSG00000233590.1] WARNING, no entry stored in dbm for [ENSG00000243538.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000230116.1] WARNING, no entry stored in dbm for [ENSG00000240992.1] WARNING, no entry stored in dbm for [ENSG00000233072.1] WARNING, no entry stored in dbm for [ENSG00000214535.3] WARNING, no entry stored in dbm for [ENSG00000237745.1] WARNING, no entry stored in dbm for [ENSG00000230171.1] WARNING, no entry stored in dbm for [ENSG00000213935.3] WARNING, no entry stored in dbm for [ENSG00000235266.1] WARNING, no entry stored in dbm for [ENSG00000203993.6] WARNING, no entry stored in dbm for [ENSG00000285492.1] WARNING, no entry stored in dbm for [ENSG00000273129.2] WARNING, no entry stored in dbm for [ENSG00000247121.7] 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 [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000267882.2] WARNING, no entry stored in dbm for [ENSG00000259275.4] WARNING, no entry stored in dbm for [ENSG00000214807.2] WARNING, no entry stored in dbm for [ENSG00000226703.1] WARNING, no entry stored in dbm for [ENSG00000224081.9] WARNING, no entry stored in dbm for [ENSG00000253230.9] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000261801.6] WARNING, no entry stored in dbm for [ENSG00000234634.2] WARNING, no entry stored in dbm for [ENSG00000237339.5] WARNING, no entry stored in dbm for [ENSG00000235687.9] WARNING, no entry stored in dbm for [ENSG00000279811.1] WARNING, no entry stored in dbm for [ENSG00000206192.7] WARNING, no entry stored in dbm for [ENSG00000266179.2] 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 [ENSG00000258673.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000249072.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000249072.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000249072.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000249072.1] 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 [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000227908.3] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000273082.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000181984.11] WARNING, no entry stored in dbm for [ENSG00000286694.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000258498.8] WARNING, no entry stored in dbm for [ENSG00000286340.1] WARNING, no entry stored in dbm for [ENSG00000203993.6] WARNING, no entry stored in dbm for [ENSG00000273668.1] WARNING, no entry stored in dbm for [ENSG00000237480.3] WARNING, no entry stored in dbm for [ENSG00000231883.1] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000287460.1] WARNING, no entry stored in dbm for [ENSG00000287559.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000231549.1] WARNING, no entry stored in dbm for [ENSG00000287215.1] WARNING, no entry stored in dbm for [ENSG00000274502.1] WARNING, no entry stored in dbm for [ENSG00000215559.8] WARNING, no entry stored in dbm for [ENSG00000228685.1] WARNING, no entry stored in dbm for [ENSG00000234851.4] WARNING, no entry stored in dbm for [ENSG00000237445.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000234996.4] WARNING, no entry stored in dbm for [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000201428.1] WARNING, no entry stored in dbm for [ENSG00000230869.1] WARNING, no entry stored in dbm for [ENSG00000283345.1] WARNING, no entry stored in dbm for [ENSG00000215302.8] WARNING, no entry stored in dbm for [ENSG00000278408.1] WARNING, no entry stored in dbm for [ENSG00000286152.1] WARNING, no entry stored in dbm for [ENSG00000258320.1] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000264151.6] WARNING, no entry stored in dbm for [ENSG00000253408.6] WARNING, no entry stored in dbm for [ENSG00000234129.8] WARNING, no entry stored in dbm for [ENSG00000268729.1] WARNING, no entry stored in dbm for [ENSG00000205682.2] WARNING, no entry stored in dbm for [ENSG00000248540.3] WARNING, no entry stored in dbm for [ENSG00000245317.2] WARNING, no entry stored in dbm for [ENSG00000260041.5] WARNING, no entry stored in dbm for [ENSG00000229110.1] WARNING, no entry stored in dbm for [ENSG00000239345.2] * STAR-Fusion complete. See output: /tmp/nxf.h2FlaRn7Dp/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)