-ctat genome lib [/tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.u40WPu7mh6/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary -sample contains 73627138 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir -J /tmp/nxf.u40WPu7mh6/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.u40WPu7mh6/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=66666.67/min [30000], rate=66666.67/min [40000], rate=66666.67/min [50000], rate=61224.49/min [60000], rate=60000.00/min [70000], rate=59154.93/min [80000], rate=59259.26/min [90000], rate=60674.16/min [100000], rate=60000.00/min [110000], rate=49624.06/min [120000], rate=45569.62/min [130000], rate=43093.92/min [140000], rate=40776.70/min [150000], rate=38461.54/min [160000], rate=38400.00/min [170000], rate=38490.57/min [180000], rate=38571.43/min [190000], rate=38644.07/min [200000], rate=38338.66/min [210000], rate=38532.11/min [220000], rate=39053.25/min [230000], rate=39884.39/min [240000], rate=41142.86/min [250000], rate=42372.88/min [260000], rate=43575.42/min [270000], rate=44751.38/min [280000], rate=45776.57/min [290000], rate=46648.79/min [300000], rate=47619.05/min [310000], rate=48311.69/min [320000], rate=49104.86/min [330000], rate=49748.74/min [340000], rate=50746.27/min [350000], rate=51724.14/min [360000], rate=52554.74/min [370000], rate=53237.41/min [380000], rate=53900.71/min [390000], rate=54041.57/min [400000], rate=54919.91/min [410000], rate=55280.90/min [420000], rate=53846.15/min [430000], rate=52439.02/min [440000], rate=51866.40/min [450000], rate=51724.14/min [460000], rate=51396.65/min [470000], rate=51272.73/min [480000], rate=51063.83/min [490000], rate=51219.51/min [500000], rate=51457.98/min [510000], rate=51602.02/min [520000], rate=50485.44/min [530000], rate=49687.50/min [540000], rate=49016.64/min [550000], rate=48104.96/min [560000], rate=47931.53/min [570000], rate=47698.74/min [580000], rate=47736.63/min [590000], rate=47773.28/min [600000], rate=47872.34/min [610000], rate=47968.55/min [620000], rate=48249.03/min [630000], rate=48523.75/min [640000], rate=48979.59/min [650000], rate=48628.43/min [660000], rate=47826.09/min [670000], rate=47238.54/min [680000], rate=46788.99/min [690000], rate=46621.62/min [700000], rate=46511.63/min [710000], rate=46506.55/min [720000], rate=46551.72/min [730000], rate=46398.31/min [740000], rate=46394.98/min [750000], rate=46296.30/min [760000], rate=45875.25/min [770000], rate=45427.73/min [780000], rate=45173.75/min [790000], rate=45099.90/min [800000], rate=45028.14/min [810000], rate=45000.00/min [820000], rate=45013.72/min [830000], rate=45027.12/min [840000], rate=45283.02/min [850000], rate=45576.41/min [860000], rate=45704.16/min [870000], rate=45829.68/min [880000], rate=46073.30/min [890000], rate=46113.99/min [900000], rate=45492.84/min [910000], rate=45012.37/min [920000], rate=44805.19/min [930000], rate=44568.69/min [940000], rate=44479.50/min [950000], rate=44496.49/min [960000], rate=44410.18/min [970000], rate=44258.56/min [980000], rate=44144.14/min [990000], rate=44065.28/min [1000000], rate=44085.23/min [1010000], rate=44169.10/min [1020000], rate=44155.84/min [1030000], rate=44237.65/min [1040000], rate=44381.22/min [1050000], rate=44585.99/min [1060000], rate=44757.21/min [1070000], rate=44769.87/min [1080000], rate=44536.08/min [1090000], rate=44459.55/min [1100000], rate=44414.54/min [1110000], rate=44429.62/min [1120000], rate=44503.31/min [1130000], rate=44575.94/min [1140000], rate=44676.68/min [1150000], rate=44834.31/min [1160000], rate=44990.30/min [1170000], rate=45057.77/min [1180000], rate=44952.38/min [1190000], rate=44877.44/min [1200000], rate=44776.12/min [1210000], rate=44676.92/min [1220000], rate=44579.78/min [1230000], rate=44619.11/min [1240000], rate=44684.68/min [1250000], rate=44749.40/min [1260000], rate=44813.28/min [1270000], rate=45008.86/min [1280000], rate=45336.48/min [1290000], rate=45609.90/min [1300000], rate=45801.53/min [1310000], rate=45964.91/min [1320000], rate=46126.97/min [1330000], rate=46234.07/min [1340000], rate=46180.36/min [1350000], rate=46206.50/min [1360000], rate=46442.80/min [1370000], rate=46440.68/min [1380000], rate=46438.59/min [1390000], rate=46514.22/min [1400000], rate=46614.87/min [1410000], rate=46714.52/min [1420000], rate=46864.69/min [1430000], rate=47065.28/min [1440000], rate=47316.54/min [1450000], rate=47463.18/min [1460000], rate=47634.58/min -building interval tree based on /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.13 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=60000.00/min [30000], rate=39130.43/min [40000], rate=34285.71/min [50000], rate=30000.00/min [60000], rate=29268.29/min [70000], rate=29577.46/min [80000], rate=30379.75/min [90000], rate=30681.82/min [100000], rate=31250.00/min [110000], rate=32195.12/min [120000], rate=32727.27/min [130000], rate=33050.85/min [140000], rate=33734.94/min [150000], rate=33582.09/min [160000], rate=33922.26/min [170000], rate=34459.46/min [180000], rate=35179.15/min [190000], rate=36305.73/min [200000], rate=37383.18/min [210000], rate=37837.84/min [220000], rate=35675.68/min [230000], rate=34586.47/min [240000], rate=33802.82/min [250000], rate=32967.03/min [260000], rate=32842.11/min [270000], rate=32727.27/min [280000], rate=32369.94/min [290000], rate=32342.01/min [300000], rate=31634.45/min [310000], rate=31525.42/min [320000], rate=30967.74/min [330000], rate=30889.24/min [340000], rate=30584.71/min [350000], rate=30478.96/min [360000], rate=30508.47/min [370000], rate=30747.92/min [380000], rate=30978.26/min [390000], rate=31241.66/min [400000], rate=31537.45/min [410000], rate=31865.28/min [420000], rate=32225.06/min [430000], rate=32575.76/min [440000], rate=33000.00/min [450000], rate=33292.23/min [460000], rate=33906.63/min [470000], rate=34558.82/min [480000], rate=35079.17/min [490000], rate=35421.69/min [500000], rate=35756.85/min [510000], rate=36127.51/min [520000], rate=35697.94/min [530000], rate=35176.99/min [540000], rate=34504.79/min [550000], rate=33915.72/min [560000], rate=33432.84/min [570000], rate=33431.09/min [580000], rate=33142.86/min [590000], rate=32930.23/min [600000], rate=32846.72/min [610000], rate=32913.67/min [620000], rate=32891.25/min [630000], rate=32869.57/min [640000], rate=32904.88/min [650000], rate=32911.39/min [660000], rate=33027.52/min [670000], rate=33195.71/min [680000], rate=33442.62/min [690000], rate=33713.36/min [700000], rate=33980.58/min [710000], rate=33569.74/min [720000], rate=33307.63/min [730000], rate=33056.60/min [740000], rate=32840.24/min [750000], rate=32679.74/min [760000], rate=32524.96/min [770000], rate=32421.05/min [780000], rate=32522.59/min [790000], rate=32622.16/min [800000], rate=32586.56/min [810000], rate=32661.29/min [820000], rate=32778.15/min [830000], rate=32827.95/min [840000], rate=32919.66/min [850000], rate=32945.74/min [860000], rate=32992.33/min [870000], rate=33100.82/min [880000], rate=33228.45/min [890000], rate=33395.87/min [900000], rate=33707.87/min [910000], rate=33891.99/min [920000], rate=34032.06/min [930000], rate=34254.14/min [940000], rate=34453.27/min [950000], rate=34420.29/min [960000], rate=34491.02/min [970000], rate=34581.11/min [980000], rate=34731.25/min [990000], rate=34859.15/min [1000000], rate=35005.83/min [1010000], rate=35150.81/min [1020000], rate=35314.48/min [1030000], rate=35456.11/min [1040000], rate=35738.83/min [1050000], rate=35979.44/min [1060000], rate=36177.47/min [1070000], rate=36291.69/min [1080000], rate=36465.95/min [1090000], rate=36597.65/min [1100000], rate=36809.82/min [1110000], rate=36979.46/min [1120000], rate=37086.09/min [1130000], rate=37334.80/min [1140000], rate=37623.76/min [1150000], rate=37891.27/min [1160000], rate=37949.84/min [1170000], rate=37987.01/min [1180000], rate=38167.12/min [1190000], rate=38304.72/min [1200000], rate=38441.00/min [1210000], rate=38596.49/min [1220000], rate=38730.16/min [1230000], rate=39006.34/min [1240000], rate=39219.82/min [1250000], rate=39411.46/min [1260000], rate=39519.08/min [1270000], rate=39687.50/min [1280000], rate=39834.02/min [1290000], rate=40062.11/min [1300000], rate=40185.47/min [1310000], rate=40328.37/min [1320000], rate=40553.00/min [1330000], rate=40797.55/min [1340000], rate=41041.35/min [1350000], rate=41263.37/min [1360000], rate=41337.39/min [1370000], rate=41389.73/min [1380000], rate=41524.57/min [1390000], rate=41616.77/min [1400000], rate=41708.04/min [1410000], rate=41860.47/min [1420000], rate=42094.86/min [1430000], rate=42286.84/min [1440000], rate=42415.32/min [1450000], rate=42542.79/min [1460000], rate=42731.71/min [1470000], rate=42961.52/min [1480000], rate=43211.68/min -building interval tree based on /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=85714.29/min [30000], rate=90000.00/min [40000], rate=88888.89/min [50000], rate=90909.09/min [60000], rate=97297.30/min [70000], rate=107692.31/min [80000], rate=114285.71/min [90000], rate=114893.62/min [100000], rate=111111.11/min [110000], rate=115789.47/min [120000], rate=124137.93/min [130000], rate=132203.39/min [140000], rate=137704.92/min [150000], rate=132352.94/min [160000], rate=126315.79/min [170000], rate=125925.93/min [180000], rate=122727.27/min [190000], rate=120000.00/min [200000], rate=117647.06/min [210000], rate=122330.10/min [220000], rate=122222.22/min [230000], rate=123214.29/min [240000], rate=122033.90/min [250000], rate=122950.82/min [260000], rate=125806.45/min [270000], rate=129600.00/min [280000], rate=133333.33/min [290000], rate=132824.43/min [300000], rate=130434.78/min [310000], rate=128275.86/min [320000], rate=127152.32/min [330000], rate=125316.46/min [340000], rate=124390.24/min [350000], rate=125748.50/min [360000], rate=126315.79/min [370000], rate=128323.70/min [380000], rate=127374.30/min [390000], rate=126486.49/min [400000], rate=128342.25/min [410000], rate=127461.14/min [420000], rate=125373.13/min [430000], rate=124637.68/min [440000], rate=123364.49/min [450000], rate=121621.62/min [460000], rate=120524.02/min [470000], rate=122608.70/min [480000], rate=122033.90/min [490000], rate=123012.55/min [500000], rate=121951.22/min [510000], rate=121912.35/min [520000], rate=122352.94/min [530000], rate=100632.91/min [540000], rate=87804.88/min [550000], rate=77283.37/min [560000], rate=69854.47/min [570000], rate=65267.18/min [580000], rate=61159.93/min [590000], rate=57937.81/min [600000], rate=55214.72/min [610000], rate=52813.85/min [620000], rate=50819.67/min [630000], rate=49802.37/min [640000], rate=48854.96/min [650000], rate=48088.78/min [660000], rate=47596.15/min [670000], rate=46473.99/min [680000], rate=45997.75/min [690000], rate=45196.51/min [700000], rate=44967.88/min [710000], rate=44794.95/min [720000], rate=44674.25/min [730000], rate=44693.88/min [740000], rate=44533.60/min [750000], rate=44422.51/min [760000], rate=44271.84/min [770000], rate=43874.64/min [780000], rate=43333.33/min [790000], rate=43130.12/min [800000], rate=42780.75/min [810000], rate=42408.38/min [820000], rate=42340.79/min [830000], rate=42310.96/min [840000], rate=42140.47/min [850000], rate=42113.96/min [860000], rate=42122.45/min [870000], rate=42130.75/min [880000], rate=42172.52/min [890000], rate=42280.29/min [900000], rate=41925.47/min [910000], rate=41679.39/min [920000], rate=41348.31/min [930000], rate=40969.16/min [940000], rate=40839.97/min [950000], rate=40830.95/min [960000], rate=40880.06/min [970000], rate=40928.27/min [980000], rate=41032.80/min [990000], rate=41192.79/min [1000000], rate=41237.11/min [1010000], rate=41056.91/min [1020000], rate=40991.29/min [1030000], rate=40981.43/min [1040000], rate=40971.77/min [1050000], rate=40962.29/min [1060000], rate=40979.38/min [1070000], rate=41022.36/min [1080000], rate=41142.86/min [1090000], rate=41340.08/min [1100000], rate=41509.43/min [1110000], rate=41729.32/min [1120000], rate=41353.85/min [1130000], rate=40720.72/min [1140000], rate=40188.01/min [1150000], rate=39930.56/min [1160000], rate=39771.43/min [1170000], rate=39571.59/min [1180000], rate=39464.88/min [1190000], rate=39447.51/min [1200000], rate=39430.45/min [1210000], rate=39370.93/min [1220000], rate=39228.30/min [1230000], rate=39088.98/min [1240000], rate=38932.50/min [1250000], rate=38839.98/min [1260000], rate=38769.23/min [1270000], rate=38660.58/min [1280000], rate=38573.58/min [1290000], rate=38488.31/min [1300000], rate=38442.58/min [1310000], rate=38378.91/min [1320000], rate=38372.09/min [1330000], rate=38365.38/min [1340000], rate=38303.95/min [1350000], rate=38243.63/min [1360000], rate=38059.70/min [1370000], rate=37897.65/min [1380000], rate=37842.78/min [1390000], rate=37805.98/min [1400000], rate=37752.81/min [1410000], rate=37683.74/min [1420000], rate=37566.14/min [1430000], rate=37483.62/min [1440000], rate=37386.41/min [1450000], rate=37435.46/min [1460000], rate=37451.90/min [1470000], rate=37484.06/min -building interval tree based on /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.13 min). -mapping reads to genes [10000], rate=33333.33/min [20000], rate=35294.12/min [30000], rate=31034.48/min [40000], rate=28235.29/min [50000], rate=28037.38/min [60000], rate=27067.67/min [70000], rate=28000.00/min [80000], rate=27906.98/min [90000], rate=26865.67/min [100000], rate=27522.94/min [110000], rate=28326.18/min [120000], rate=28235.29/min [130000], rate=28571.43/min [140000], rate=28187.92/min [150000], rate=28571.43/min [160000], rate=27586.21/min [170000], rate=27717.39/min [180000], rate=27979.27/min [190000], rate=28217.82/min [200000], rate=28301.89/min [210000], rate=28187.92/min [220000], rate=28387.10/min [230000], rate=28630.71/min [240000], rate=28742.51/min [250000], rate=28463.00/min [260000], rate=28363.64/min [270000], rate=28521.13/min [280000], rate=28474.58/min [290000], rate=28431.37/min [300000], rate=28391.17/min [310000], rate=28396.95/min [320000], rate=28402.37/min [330000], rate=28530.26/min [340000], rate=28372.74/min [350000], rate=28532.61/min [360000], rate=28685.26/min [370000], rate=28831.17/min [380000], rate=28934.01/min [390000], rate=28960.40/min [400000], rate=28673.84/min [410000], rate=28406.47/min [420000], rate=28539.07/min [430000], rate=28476.82/min [440000], rate=28633.41/min [450000], rate=28511.09/min [460000], rate=28541.88/min [470000], rate=28513.65/min [480000], rate=28599.80/min [490000], rate=28654.97/min [500000], rate=28680.69/min [510000], rate=28624.88/min [520000], rate=28571.43/min [530000], rate=28597.12/min [540000], rate=28521.13/min [550000], rate=28546.71/min [560000], rate=28522.92/min [570000], rate=28643.22/min [580000], rate=28571.43/min [590000], rate=28502.42/min [600000], rate=28594.12/min [610000], rate=28660.92/min [620000], rate=28681.57/min [630000], rate=28658.07/min [640000], rate=28678.12/min [650000], rate=28446.39/min [660000], rate=28448.28/min [670000], rate=28470.25/min [680000], rate=28471.74/min [690000], rate=28512.40/min [700000], rate=28532.61/min [710000], rate=28494.98/min [720000], rate=28609.27/min [730000], rate=28571.43/min [740000], rate=28608.25/min [750000], rate=28625.95/min [760000], rate=28715.37/min [770000], rate=28802.99/min [780000], rate=28906.73/min [790000], rate=28920.07/min [800000], rate=28950.54/min [810000], rate=28945.80/min [820000], rate=28958.21/min [830000], rate=28970.33/min [840000], rate=28932.26/min [850000], rate=28977.27/min [860000], rate=28810.72/min [870000], rate=28681.32/min [880000], rate=28602.38/min [890000], rate=28540.89/min [900000], rate=28632.03/min [910000], rate=28706.62/min [920000], rate=28720.08/min [930000], rate=28807.43/min [940000], rate=28908.25/min [950000], rate=28992.88/min [960000], rate=29046.90/min [970000], rate=29158.32/min [980000], rate=29239.18/min [990000], rate=29391.39/min [1000000], rate=29556.65/min [1010000], rate=29735.03/min [1020000], rate=29897.41/min [1030000], rate=29985.44/min [1040000], rate=29856.46/min [1050000], rate=29773.16/min [1060000], rate=29664.18/min [1070000], rate=29749.77/min [1080000], rate=29765.73/min [1090000], rate=29849.38/min [1100000], rate=29904.85/min [1110000], rate=29946.04/min [1120000], rate=29933.18/min [1130000], rate=29920.56/min [1140000], rate=29947.46/min [1150000], rate=29986.96/min [1160000], rate=30051.81/min [1170000], rate=30154.64/min [1180000], rate=30282.29/min [1190000], rate=30421.82/min [1200000], rate=30573.25/min [1210000], rate=30736.66/min [1220000], rate=30886.08/min [1230000], rate=31047.54/min [1240000], rate=31181.89/min [1250000], rate=31315.24/min [1260000], rate=31460.67/min [1270000], rate=31605.14/min [1280000], rate=31748.66/min [1290000], rate=31904.37/min [1300000], rate=31993.44/min [1310000], rate=32068.54/min [1320000], rate=32155.91/min [1330000], rate=32242.42/min [1340000], rate=32354.12/min [1350000], rate=32464.93/min [1360000], rate=32600.88/min [1370000], rate=32735.96/min [1380000], rate=32909.38/min [1390000], rate=32977.46/min [1400000], rate=33018.87/min [1410000], rate=33059.79/min [1420000], rate=33190.49/min [1430000], rate=33268.71/min [1440000], rate=33346.20/min [1450000], rate=33435.82/min [1460000], rate=33537.52/min [1470000], rate=33651.28/min [1480000], rate=33777.10/min [1490000], rate=33735.85/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir --filt_file /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 6000000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 4500000.00 reads per min processed... 3818181.82 reads per min processed... 3200000.00 reads per min processed... 3176470.59 reads per min processed... 3157894.74 reads per min processed... 3000000.00 reads per min processed... 2769230.77 reads per min processed... 2689655.17 reads per min processed... 2625000.00 reads per min processed... 2500000.00 reads per min processed... 2461538.46 reads per min processed... 2428571.43 reads per min processed... 2347826.09 reads per min processed... 2326530.61 reads per min processed... 2307692.31 reads per min processed... 2250000.00 reads per min processed... 2315789.47 reads per min processed... 2300000.00 reads per min processed... 2322580.65 reads per min processed... 2343750.00 reads per min processed... 2328358.21 reads per min processed... 2347826.09 reads per min processed... 2333333.33 reads per min processed... 2351351.35 reads per min processed... 2337662.34 reads per min processed... 2354430.38 reads per min processed... 2370370.37 reads per min processed... 2385542.17 reads per min processed... 2400000.00 reads per min processed... 2413793.10 reads per min processed... 2400000.00 reads per min processed... 2439560.44 reads per min processed... 2478260.87 reads per min processed... 2516129.03 reads per min processed... 2553191.49 reads per min processed... 2562500.00 reads per min processed... 2571428.57 reads per min processed... 2580000.00 reads per min processed... 2563106.80 reads per min processed... 2571428.57 reads per min processed... 2555555.56 reads per min processed... 2540540.54 reads per min processed... 2548672.57 reads per min processed... 2556521.74 reads per min processed... 2564102.56 reads per min processed... 2571428.57 reads per min processed... 2578512.40 reads per min processed... 2585365.85 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.u40WPu7mh6/SkinN_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.u40WPu7mh6/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -62760.351527 EM: Round [1] log likelihood: -62632.485188 EM: Round [2] log likelihood: -62577.763568 EM: Round [3] log likelihood: -62549.768434 EM: Round [4] log likelihood: -62534.376421 EM: Round [5] log likelihood: -62525.603104 EM: Round [6] log likelihood: -62520.453753 EM: Round [7] log likelihood: -62517.330758 EM: Round [8] log likelihood: -62515.367041 EM: Round [9] log likelihood: -62514.086365 EM: Round [10] log likelihood: -62513.221849 EM: Round [11] log likelihood: -62512.619741 EM: Round [12] log likelihood: -62512.188630 EM: Round [13] log likelihood: -62511.872385 EM: Round [14] log likelihood: -62511.635446 EM: Round [15] log likelihood: -62511.454610 EM: Round [16] log likelihood: -62511.314330 EM: Round [17] log likelihood: -62511.203927 EM: Round [18] log likelihood: -62511.115908 EM: Round [19] log likelihood: -62511.044907 EM: Round [20] log likelihood: -62510.987020 EM: Round [21] log likelihood: -62510.939358 EM: Round [22] log likelihood: -62510.899756 EM: Round [23] log likelihood: -62510.866568 EM: Round [24] log likelihood: -62510.838532 EM: Round [25] log likelihood: -62510.814669 EM: Round [26] log likelihood: -62510.794212 EM: Round [27] log likelihood: -62510.776555 EM: Round [28] log likelihood: -62510.761218 EM: Round [29] log likelihood: -62510.747814 EM: Round [30] log likelihood: -62510.736031 EM: Round [31] log likelihood: -62510.725618 EM: Round [32] log likelihood: -62510.716367 EM: Round [33] log likelihood: -62510.708108 EM: Round [34] log likelihood: -62510.700703 EM: Round [35] log likelihood: -62510.694034 EM: Round [36] log likelihood: -62510.688004 EM: Round [37] log likelihood: -62510.682532 EM: Round [38] log likelihood: -62510.677550 EM: Round [39] log likelihood: -62510.673000 EM: Round [40] log likelihood: -62510.668831 EM: Round [41] log likelihood: -62510.665002 EM: Round [42] log likelihood: -62510.661477 EM: Round [43] log likelihood: -62510.658224 EM: Round [44] log likelihood: -62510.655215 EM: Round [45] log likelihood: -62510.652428 EM: Round [46] log likelihood: -62510.649842 EM: Round [47] log likelihood: -62510.647438 EM: Round [48] log likelihood: -62510.645201 EM: Round [49] log likelihood: -62510.643115 EM: Round [50] log likelihood: -62510.641169 EM: Round [51] log likelihood: -62510.639352 EM: Round [52] log likelihood: -62510.637652 EM: Round [53] log likelihood: -62510.636061 EM: Round [54] log likelihood: -62510.634572 EM: Round [55] log likelihood: -62510.633175 EM: Round [56] log likelihood: -62510.631865 EM: Round [57] log likelihood: -62510.630635 EM: Round [58] log likelihood: -62510.629480 EM: Round [59] log likelihood: -62510.628394 EM: Round [60] log likelihood: -62510.627374 EM: Round [61] log likelihood: -62510.626414 EM: Round [62] log likelihood: -62510.625510 EM: Round [63] log likelihood: -62510.624659 EM: Round [64] log likelihood: -62510.623858 EM: Round [65] log likelihood: -62510.623103 EM: Round [66] log likelihood: -62510.622392 EM: Round [67] log likelihood: -62510.621721 EM: Round [68] log likelihood: -62510.621088 EM: Round [69] log likelihood: -62510.620491 EM: Round [70] log likelihood: -62510.619928 EM: Round [71] log likelihood: -62510.619396 EM: Round [72] log likelihood: -62510.618894 EM: Round [73] log likelihood: -62510.618419 EM: Round [74] log likelihood: -62510.617971 EM: Round [75] log likelihood: -62510.617548 EM: Round [76] log likelihood: -62510.617148 EM: Round [77] log likelihood: -62510.616770 EM: Round [78] log likelihood: -62510.616412 EM: Round [79] log likelihood: -62510.616074 EM: Round [80] log likelihood: -62510.615755 EM: Round [81] log likelihood: -62510.615452 EM: Round [82] log likelihood: -62510.615166 EM: Round [83] log likelihood: -62510.614895 EM: Round [84] log likelihood: -62510.614638 EM: Round [85] log likelihood: -62510.614395 EM: Round [86] log likelihood: -62510.614165 EM: Round [87] log likelihood: -62510.613947 EM: Round [88] log likelihood: -62510.613741 EM: Round [89] log likelihood: -62510.613546 EM: Round [90] log likelihood: -62510.613360 EM: Round [91] log likelihood: -62510.613185 EM: Round [92] log likelihood: -62510.613018 EM: Round [93] log likelihood: -62510.612861 EM: Round [94] log likelihood: -62510.612711 EM: Round [95] log likelihood: -62510.612569 EM: Round [96] log likelihood: -62510.612434 EM: Round [97] log likelihood: -62510.612307 EM: Round [98] log likelihood: -62510.612185 EM: Round [99] log likelihood: -62510.612070 EM: Round [100] log likelihood: -62510.611961 EM: Round [101] log likelihood: -62510.611858 EM: Round [102] log likelihood: -62510.611759 EM: Stopping iterations at round 102 due to insufficient improvement in likelihood. EM: Starting log likelihood: -62692.539102 EM: Round [1] log likelihood: -62585.041446 EM: Round [2] log likelihood: -62541.752696 EM: Round [3] log likelihood: -62520.193369 EM: Round [4] log likelihood: -62508.480264 EM: Round [5] log likelihood: -62501.855656 EM: Round [6] log likelihood: -62497.995443 EM: Round [7] log likelihood: -62495.672100 EM: Round [8] log likelihood: -62494.223143 EM: Round [9] log likelihood: -62493.286348 EM: Round [10] log likelihood: -62492.659629 EM: Round [11] log likelihood: -62492.227112 EM: Round [12] log likelihood: -62491.920246 EM: Round [13] log likelihood: -62491.697154 EM: Round [14] log likelihood: -62491.531445 EM: Round [15] log likelihood: -62491.405991 EM: Round [16] log likelihood: -62491.309383 EM: Round [17] log likelihood: -62491.233833 EM: Round [18] log likelihood: -62491.173914 EM: Round [19] log likelihood: -62491.125769 EM: Round [20] log likelihood: -62491.086614 EM: Round [21] log likelihood: -62491.054408 EM: Round [22] log likelihood: -62491.027633 EM: Round [23] log likelihood: -62491.005149 EM: Round [24] log likelihood: -62490.986088 EM: Round [25] log likelihood: -62490.969784 EM: Round [26] log likelihood: -62490.955719 EM: Round [27] log likelihood: -62490.943491 EM: Round [28] log likelihood: -62490.932779 EM: Round [29] log likelihood: -62490.923330 EM: Round [30] log likelihood: -62490.914941 EM: Round [31] log likelihood: -62490.907448 EM: Round [32] log likelihood: -62490.900718 EM: Round [33] log likelihood: -62490.894642 EM: Round [34] log likelihood: -62490.889132 EM: Round [35] log likelihood: -62490.884112 EM: Round [36] log likelihood: -62490.879522 EM: Round [37] log likelihood: -62490.875310 EM: Round [38] log likelihood: -62490.871432 EM: Round [39] log likelihood: -62490.867852 EM: Round [40] log likelihood: -62490.864538 EM: Round [41] log likelihood: -62490.861463 EM: Round [42] log likelihood: -62490.858605 EM: Round [43] log likelihood: -62490.855942 EM: Round [44] log likelihood: -62490.853458 EM: Round [45] log likelihood: -62490.851137 EM: Round [46] log likelihood: -62490.848965 EM: Round [47] log likelihood: -62490.846930 EM: Round [48] log likelihood: -62490.845023 EM: Round [49] log likelihood: -62490.843232 EM: Round [50] log likelihood: -62490.841550 EM: Round [51] log likelihood: -62490.839969 EM: Round [52] log likelihood: -62490.838481 EM: Round [53] log likelihood: -62490.837081 EM: Round [54] log likelihood: -62490.835762 EM: Round [55] log likelihood: -62490.834519 EM: Round [56] log likelihood: -62490.833348 EM: Round [57] log likelihood: -62490.832243 EM: Round [58] log likelihood: -62490.831201 EM: Round [59] log likelihood: -62490.830218 EM: Round [60] log likelihood: -62490.829290 EM: Round [61] log likelihood: -62490.828413 EM: Round [62] log likelihood: -62490.827585 EM: Round [63] log likelihood: -62490.826803 EM: Round [64] log likelihood: -62490.826064 EM: Round [65] log likelihood: -62490.825365 EM: Round [66] log likelihood: -62490.824705 EM: Round [67] log likelihood: -62490.824081 EM: Round [68] log likelihood: -62490.823490 EM: Round [69] log likelihood: -62490.822932 EM: Round [70] log likelihood: -62490.822404 EM: Round [71] log likelihood: -62490.821904 EM: Round [72] log likelihood: -62490.821432 EM: Round [73] log likelihood: -62490.820984 EM: Round [74] log likelihood: -62490.820561 EM: Round [75] log likelihood: -62490.820160 EM: Round [76] log likelihood: -62490.819781 EM: Round [77] log likelihood: -62490.819422 EM: Round [78] log likelihood: -62490.819081 EM: Round [79] log likelihood: -62490.818759 EM: Round [80] log likelihood: -62490.818454 EM: Round [81] log likelihood: -62490.818165 EM: Round [82] log likelihood: -62490.817891 EM: Round [83] log likelihood: -62490.817632 EM: Round [84] log likelihood: -62490.817386 EM: Round [85] log likelihood: -62490.817153 EM: Round [86] log likelihood: -62490.816932 EM: Round [87] log likelihood: -62490.816723 EM: Round [88] log likelihood: -62490.816524 EM: Round [89] log likelihood: -62490.816336 EM: Round [90] log likelihood: -62490.816158 EM: Round [91] log likelihood: -62490.815989 EM: Round [92] log likelihood: -62490.815828 EM: Round [93] log likelihood: -62490.815676 EM: Round [94] log likelihood: -62490.815532 EM: Round [95] log likelihood: -62490.815394 EM: Round [96] log likelihood: -62490.815264 EM: Round [97] log likelihood: -62490.815141 EM: Round [98] log likelihood: -62490.815024 EM: Round [99] log likelihood: -62490.814913 EM: Round [100] log likelihood: -62490.814807 EM: Round [101] log likelihood: -62490.814707 EM: Round [102] log likelihood: -62490.814612 EM: Stopping iterations at round 102 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.u40WPu7mh6/./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.u40WPu7mh6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.u40WPu7mh6/./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.u40WPu7mh6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 73627138 > /tmp/nxf.u40WPu7mh6/./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.u40WPu7mh6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir > /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir --annotate /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.u40WPu7mh6/./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.u40WPu7mh6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir -done, see /tmp/nxf.u40WPu7mh6/./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.u40WPu7mh6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.u40WPu7mh6/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 303, filtered: 3346) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.u40WPu7mh6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.u40WPu7mh6/./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.u40WPu7mh6/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000229739.4] WARNING, no entry stored in dbm for [ENSG00000286907.1] WARNING, no entry stored in dbm for [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000264618.2] WARNING, no entry stored in dbm for [ENSG00000240869.3] WARNING, no entry stored in dbm for [ENSG00000242559.3] WARNING, no entry stored in dbm for [ENSG00000240869.3] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000229699.1] WARNING, no entry stored in dbm for [ENSG00000271776.1] WARNING, no entry stored in dbm for [ENSG00000271776.1] WARNING, no entry stored in dbm for [ENSG00000271776.1] WARNING, no entry stored in dbm for [ENSG00000271776.1] WARNING, no entry stored in dbm for [ENSG00000273084.1] WARNING, no entry stored in dbm for [ENSG00000234230.1] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000223806.8] WARNING, no entry stored in dbm for [ENSG00000224498.1] WARNING, no entry stored in dbm for [ENSG00000276805.2] WARNING, no entry stored in dbm for [ENSG00000270641.1] WARNING, no entry stored in dbm for [ENSG00000256092.2] WARNING, no entry stored in dbm for [ENSG00000287243.2] WARNING, no entry stored in dbm for [ENSG00000287243.2] WARNING, no entry stored in dbm for [ENSG00000197558.13] WARNING, no entry stored in dbm for [ENSG00000236901.6] WARNING, no entry stored in dbm for [ENSG00000275090.1] WARNING, no entry stored in dbm for [ENSG00000265182.1] WARNING, no entry stored in dbm for [ENSG00000283426.1] WARNING, no entry stored in dbm for [ENSG00000185485.14] WARNING, no entry stored in dbm for [ENSG00000267323.1] WARNING, no entry stored in dbm for [ENSG00000185485.14] WARNING, no entry stored in dbm for [ENSG00000277739.1] WARNING, no entry stored in dbm for [ENSG00000257671.1] WARNING, no entry stored in dbm for [ENSG00000287949.1] WARNING, no entry stored in dbm for [ENSG00000250308.2] WARNING, no entry stored in dbm for [ENSG00000250308.2] WARNING, no entry stored in dbm for [ENSG00000276417.1] WARNING, no entry stored in dbm for [ENSG00000269352.1] WARNING, no entry stored in dbm for [ENSG00000231760.5] WARNING, no entry stored in dbm for [ENSG00000200296.1] WARNING, no entry stored in dbm for [ENSG00000266828.2] WARNING, no entry stored in dbm for [ENSG00000275090.1] WARNING, no entry stored in dbm for [ENSG00000266439.2] WARNING, no entry stored in dbm for [ENSG00000275090.1] WARNING, no entry stored in dbm for [ENSG00000266420.2] WARNING, no entry stored in dbm for [ENSG00000266420.2] WARNING, no entry stored in dbm for [ENSG00000260918.1] WARNING, no entry stored in dbm for [ENSG00000200312.1] WARNING, no entry stored in dbm for [ENSG00000200761.1] WARNING, no entry stored in dbm for [ENSG00000252963.1] WARNING, no entry stored in dbm for [ENSG00000222784.1] WARNING, no entry stored in dbm for [ENSG00000267519.6] WARNING, no entry stored in dbm for [ENSG00000230461.9] WARNING, no entry stored in dbm for [ENSG00000272195.1] WARNING, no entry stored in dbm for [ENSG00000214176.9] WARNING, no entry stored in dbm for [ENSG00000269400.1] WARNING, no entry stored in dbm for [ENSG00000287975.1] WARNING, no entry stored in dbm for [ENSG00000225377.6] WARNING, no entry stored in dbm for [ENSG00000281903.2] WARNING, no entry stored in dbm for [ENSG00000242510.1] WARNING, no entry stored in dbm for [ENSG00000240268.6] WARNING, no entry stored in dbm for [ENSG00000196312.15] WARNING, no entry stored in dbm for [ENSG00000287556.1] WARNING, no entry stored in dbm for [ENSG00000235294.1] WARNING, no entry stored in dbm for [ENSG00000247373.3] WARNING, no entry stored in dbm for [ENSG00000203688.6] WARNING, no entry stored in dbm for [ENSG00000253417.5] WARNING, no entry stored in dbm for [ENSG00000254101.7] WARNING, no entry stored in dbm for [ENSG00000237574.1] WARNING, no entry stored in dbm for [ENSG00000215866.8] WARNING, no entry stored in dbm for [ENSG00000281912.1] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000260799.1] WARNING, no entry stored in dbm for [ENSG00000279569.1] WARNING, no entry stored in dbm for [ENSG00000249072.1] WARNING, no entry stored in dbm for [ENSG00000234585.6] WARNING, no entry stored in dbm for [ENSG00000234152.1] WARNING, no entry stored in dbm for [ENSG00000251600.8] WARNING, no entry stored in dbm for [ENSG00000262769.1] WARNING, no entry stored in dbm for [ENSG00000203804.5] WARNING, no entry stored in dbm for [ENSG00000262001.1] WARNING, no entry stored in dbm for [ENSG00000273270.1] WARNING, no entry stored in dbm for [ENSG00000249072.1] WARNING, no entry stored in dbm for [ENSG00000225722.1] WARNING, no entry stored in dbm for [ENSG00000274937.1] WARNING, no entry stored in dbm for [ENSG00000267374.2] WARNING, no entry stored in dbm for [ENSG00000197308.9] WARNING, no entry stored in dbm for [ENSG00000277878.1] WARNING, no entry stored in dbm for [ENSG00000240710.1] WARNING, no entry stored in dbm for [ENSG00000226438.1] WARNING, no entry stored in dbm for [ENSG00000287887.1] WARNING, no entry stored in dbm for [ENSG00000233967.7] WARNING, no entry stored in dbm for [ENSG00000279609.1] WARNING, no entry stored in dbm for [ENSG00000220685.3] WARNING, no entry stored in dbm for [ENSG00000248697.1] WARNING, no entry stored in dbm for [ENSG00000254211.6] WARNING, no entry stored in dbm for [ENSG00000283453.2] WARNING, no entry stored in dbm for [ENSG00000284964.1] WARNING, no entry stored in dbm for [ENSG00000284808.1] WARNING, no entry stored in dbm for [ENSG00000239969.5] WARNING, no entry stored in dbm for [ENSG00000239969.5] WARNING, no entry stored in dbm for [ENSG00000197320.5] WARNING, no entry stored in dbm for [ENSG00000251131.2] WARNING, no entry stored in dbm for [ENSG00000259429.5] WARNING, no entry stored in dbm for [ENSG00000272267.2] WARNING, no entry stored in dbm for [ENSG00000286481.1] WARNING, no entry stored in dbm for [ENSG00000273098.3] WARNING, no entry stored in dbm for [ENSG00000267139.1] WARNING, no entry stored in dbm for [ENSG00000230305.2] WARNING, no entry stored in dbm for [ENSG00000250778.1] WARNING, no entry stored in dbm for [ENSG00000214243.3] * STAR-Fusion complete. See output: /tmp/nxf.u40WPu7mh6/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)