-ctat genome lib [/tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.4mWoukv9HD/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary -sample contains 138319193 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir -J /tmp/nxf.4mWoukv9HD/HeadNeckN_FFPE_L09_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.4mWoukv9HD/HeadNeckN_FFPE_L09_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=100000.00/min [30000], rate=105882.35/min [40000], rate=100000.00/min [50000], rate=65217.39/min [60000], rate=53731.34/min [70000], rate=48837.21/min [80000], rate=46601.94/min [90000], rate=45378.15/min [100000], rate=44444.44/min [110000], rate=44000.00/min [120000], rate=44171.78/min [130000], rate=43820.22/min [140000], rate=43979.06/min [150000], rate=44334.98/min [160000], rate=44651.16/min [170000], rate=44933.92/min [180000], rate=45957.45/min [190000], rate=46721.31/min [200000], rate=47808.76/min [210000], rate=48091.60/min [220000], rate=48708.49/min [230000], rate=49110.32/min [240000], rate=50174.22/min [250000], rate=50675.68/min [260000], rate=51827.24/min [270000], rate=52090.03/min [280000], rate=52173.91/min [290000], rate=52567.98/min [300000], rate=52941.18/min [310000], rate=53602.31/min [320000], rate=54084.51/min [330000], rate=54545.45/min [340000], rate=55135.14/min [350000], rate=55851.06/min [360000], rate=56692.91/min [370000], rate=57963.45/min [380000], rate=58762.89/min [390000], rate=59240.51/min [400000], rate=59850.37/min [410000], rate=60591.13/min [420000], rate=61165.05/min [430000], rate=61870.50/min [440000], rate=62411.35/min [450000], rate=62937.06/min [460000], rate=63594.47/min [470000], rate=64383.56/min [480000], rate=65011.29/min [490000], rate=65625.00/min [500000], rate=66371.68/min [510000], rate=66521.74/min [520000], rate=66666.67/min [530000], rate=66806.72/min [540000], rate=67080.75/min [550000], rate=67484.66/min [560000], rate=67878.79/min [570000], rate=68400.00/min [580000], rate=68910.89/min [590000], rate=69275.93/min [600000], rate=69767.44/min [610000], rate=70249.52/min [620000], rate=70722.43/min [630000], rate=71186.44/min [640000], rate=71641.79/min [650000], rate=72088.72/min [660000], rate=72660.55/min [670000], rate=73090.91/min [680000], rate=73779.39/min [690000], rate=74594.59/min [700000], rate=75539.57/min [710000], rate=76344.09/min [720000], rate=77280.86/min [730000], rate=78354.20/min [740000], rate=79285.71/min [750000], rate=80213.90/min [760000], rate=81138.79/min [770000], rate=82060.39/min [780000], rate=82831.86/min [790000], rate=83450.70/min [800000], rate=84358.52/min [810000], rate=85263.16/min [820000], rate=86164.62/min [830000], rate=87215.41/min [840000], rate=87958.12/min [850000], rate=88388.21/min [860000], rate=88659.79/min [870000], rate=89230.77/min [880000], rate=89643.46/min [890000], rate=89447.24/min [900000], rate=89850.25/min [910000], rate=90397.35/min [920000], rate=90789.47/min [930000], rate=91625.62/min [940000], rate=91856.68/min [950000], rate=92084.01/min [960000], rate=92160.00/min [970000], rate=92527.82/min [980000], rate=93185.42/min [990000], rate=93987.34/min [1000000], rate=94191.52/min [1010000], rate=94245.72/min [1020000], rate=94444.44/min [1030000], rate=94207.32/min [1040000], rate=93975.90/min [1050000], rate=94170.40/min [1060000], rate=94783.90/min [1070000], rate=95393.76/min [1080000], rate=95857.99/min [1090000], rate=96318.11/min [1100000], rate=96774.19/min [1110000], rate=97510.98/min [1120000], rate=98389.46/min [1130000], rate=99122.81/min [1140000], rate=99854.01/min [1150000], rate=99855.28/min [1160000], rate=100000.00/min [1170000], rate=100429.18/min [1180000], rate=100425.53/min [1190000], rate=100563.38/min [1200000], rate=100699.30/min [1210000], rate=100693.48/min [1220000], rate=100965.52/min [1230000], rate=101652.89/min [1240000], rate=102338.38/min [1250000], rate=102880.66/min [1260000], rate=103561.64/min [1270000], rate=104383.56/min [1280000], rate=105061.56/min [1290000], rate=105737.70/min [1300000], rate=106412.01/min [1310000], rate=106938.78/min [1320000], rate=107462.69/min [1330000], rate=107983.76/min [1340000], rate=108648.65/min [1350000], rate=109311.74/min [1360000], rate=110121.46/min [1370000], rate=110632.57/min [1380000], rate=111140.94/min [1390000], rate=111051.93/min [1400000], rate=111405.84/min [1410000], rate=111609.50/min [1420000], rate=111227.15/min [1430000], rate=111573.47/min [1440000], rate=111772.32/min [1450000], rate=112113.40/min [1460000], rate=112596.40/min [1470000], rate=112500.00/min [1480000], rate=112547.53/min [1490000], rate=112736.44/min [1500000], rate=112923.46/min [1510000], rate=113391.74/min [1520000], rate=113857.68/min [1530000], rate=114463.84/min [1540000], rate=115068.49/min [1550000], rate=115671.64/min [1560000], rate=116273.29/min [1570000], rate=116873.45/min [1580000], rate=117617.87/min [1590000], rate=117632.55/min [1600000], rate=117647.06/min [1610000], rate=117661.39/min [1620000], rate=117391.30/min [1630000], rate=116985.65/min [1640000], rate=117003.57/min [1650000], rate=117437.72/min [1660000], rate=117869.82/min [1670000], rate=118299.88/min [1680000], rate=118588.24/min [1690000], rate=118874.56/min [1700000], rate=119437.94/min [1710000], rate=120140.52/min [1720000], rate=120701.75/min [1730000], rate=121120.19/min [1740000], rate=121113.69/min [1750000], rate=121107.27/min [1760000], rate=121100.92/min [1770000], rate=121094.64/min [1780000], rate=120951.30/min [1790000], rate=120674.16/min [1800000], rate=120401.34/min [1810000], rate=120935.41/min [1820000], rate=121198.67/min [1830000], rate=121192.05/min [1840000], rate=121719.96/min [1850000], rate=121844.13/min [1860000], rate=121701.20/min [1870000], rate=121956.52/min [1880000], rate=121814.25/min [1890000], rate=121935.48/min [1900000], rate=122317.60/min [1910000], rate=122829.58/min [1920000], rate=122945.57/min [1930000], rate=122929.94/min [1940000], rate=122655.43/min [1950000], rate=122513.09/min [1960000], rate=122500.00/min [1970000], rate=122614.11/min [1980000], rate=122727.27/min [1990000], rate=122966.01/min [2000000], rate=123076.92/min [2010000], rate=123061.22/min [2020000], rate=122796.35/min [2030000], rate=122535.21/min [2040000], rate=122277.72/min [2050000], rate=122023.81/min [2060000], rate=121893.49/min [2070000], rate=121764.71/min [2080000], rate=121637.43/min [2090000], rate=121629.49/min [2100000], rate=121504.34/min [2110000], rate=121380.63/min [2120000], rate=121374.05/min [2130000], rate=121367.52/min [2140000], rate=121361.06/min [2150000], rate=119666.05/min [2160000], rate=117818.18/min [2170000], rate=116562.22/min [2180000], rate=115343.92/min [2190000], rate=114559.72/min [2200000], rate=114186.85/min [2210000], rate=112947.19/min [2220000], rate=112310.29/min [2230000], rate=110945.27/min [2240000], rate=109983.63/min [2250000], rate=109311.74/min [2260000], rate=108828.25/min [2270000], rate=108439.49/min [2280000], rate=107801.42/min -building interval tree based on /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=60000.00/min [20000], rate=50000.00/min [30000], rate=48648.65/min [40000], rate=52173.91/min [50000], rate=50847.46/min [60000], rate=51428.57/min [70000], rate=53164.56/min [80000], rate=55172.41/min [90000], rate=56842.11/min [100000], rate=59405.94/min [110000], rate=61682.24/min [120000], rate=64285.71/min [130000], rate=67241.38/min [140000], rate=69421.49/min [150000], rate=72000.00/min [160000], rate=74418.60/min [170000], rate=76691.73/min [180000], rate=78832.12/min [190000], rate=77027.03/min [200000], rate=73619.63/min [210000], rate=71186.44/min [220000], rate=68750.00/min [230000], rate=67980.30/min [240000], rate=67289.72/min [250000], rate=66964.29/min [260000], rate=66666.67/min [270000], rate=66393.44/min [280000], rate=66141.73/min [290000], rate=66412.21/min [300000], rate=66666.67/min [310000], rate=66666.67/min [320000], rate=66898.95/min [330000], rate=67346.94/min [340000], rate=68227.42/min [350000], rate=68852.46/min [360000], rate=69677.42/min [370000], rate=70476.19/min [380000], rate=70588.24/min [390000], rate=70059.88/min [400000], rate=68965.52/min [410000], rate=67029.97/min [420000], rate=66843.50/min [430000], rate=66153.85/min [440000], rate=65346.53/min [450000], rate=65060.24/min [460000], rate=64637.00/min [470000], rate=64530.89/min [480000], rate=64429.53/min [490000], rate=64615.38/min [500000], rate=64794.82/min [510000], rate=65384.62/min [520000], rate=65546.22/min [530000], rate=65975.10/min [540000], rate=66393.44/min [550000], rate=66666.67/min [560000], rate=67065.87/min [570000], rate=67455.62/min [580000], rate=67968.75/min [590000], rate=68339.77/min [600000], rate=68965.52/min [610000], rate=69581.75/min [620000], rate=70454.55/min [630000], rate=70129.87/min [640000], rate=69064.75/min [650000], rate=68661.97/min [660000], rate=68275.86/min [670000], rate=67676.77/min [680000], rate=66995.07/min [690000], rate=66346.15/min [700000], rate=65522.62/min [710000], rate=64741.64/min [720000], rate=64094.96/min [730000], rate=64035.09/min [740000], rate=64161.85/min [750000], rate=64102.56/min [760000], rate=64225.35/min [770000], rate=64345.40/min [780000], rate=64462.81/min [790000], rate=64665.76/min [800000], rate=64864.86/min [810000], rate=65060.24/min [820000], rate=65687.58/min [830000], rate=66311.58/min [840000], rate=66932.27/min [850000], rate=67193.68/min [860000], rate=67450.98/min [870000], rate=67792.21/min [880000], rate=68129.03/min [890000], rate=68461.54/min [900000], rate=68789.81/min [910000], rate=68679.25/min [920000], rate=68064.12/min [930000], rate=67391.30/min [940000], rate=66352.94/min [950000], rate=65592.64/min [960000], rate=65158.37/min [970000], rate=65100.67/min [980000], rate=64829.11/min [990000], rate=64635.47/min [1000000], rate=64377.68/min [1010000], rate=64399.57/min [1020000], rate=64421.05/min [1030000], rate=64442.13/min [1040000], rate=64529.47/min [1050000], rate=64417.18/min [1060000], rate=64437.69/min [1070000], rate=64457.83/min [1080000], rate=64413.52/min [1090000], rate=64370.08/min [1100000], rate=64390.24/min [1110000], rate=64534.88/min [1120000], rate=64802.31/min [1130000], rate=64942.53/min [1140000], rate=65204.96/min [1150000], rate=65464.90/min [1160000], rate=65722.38/min [1170000], rate=65977.44/min [1180000], rate=66292.13/min [1190000], rate=66480.45/min [1200000], rate=66728.45/min [1210000], rate=66974.17/min [1220000], rate=67217.63/min [1230000], rate=67397.26/min [1240000], rate=67697.91/min [1250000], rate=67934.78/min [1260000], rate=68231.05/min [1270000], rate=68463.61/min [1280000], rate=68694.10/min [1290000], rate=68861.21/min [1300000], rate=69087.69/min [1310000], rate=69251.10/min [1320000], rate=69473.68/min [1330000], rate=69633.51/min [1340000], rate=69852.30/min [1350000], rate=70069.20/min [1360000], rate=70284.24/min [1370000], rate=70497.43/min [1380000], rate=70708.80/min [1390000], rate=70737.91/min [1400000], rate=70886.08/min [1410000], rate=70973.15/min [1420000], rate=71118.53/min [1430000], rate=71203.32/min [1440000], rate=71346.00/min [1450000], rate=71663.92/min [1460000], rate=71803.28/min [1470000], rate=72058.82/min [1480000], rate=72312.70/min [1490000], rate=72506.08/min [1500000], rate=72756.67/min [1510000], rate=72712.68/min [1520000], rate=72496.03/min [1530000], rate=72340.43/min [1540000], rate=72243.94/min [1550000], rate=72204.97/min [1560000], rate=72110.94/min [1570000], rate=72073.45/min [1580000], rate=72091.25/min [1590000], rate=72108.84/min [1600000], rate=72180.45/min [1610000], rate=72251.31/min [1620000], rate=72375.28/min [1630000], rate=72498.15/min [1640000], rate=72673.56/min [1650000], rate=72847.68/min [1660000], rate=72967.03/min [1670000], rate=73192.11/min [1680000], rate=73415.88/min [1690000], rate=73584.91/min [1700000], rate=73752.71/min [1710000], rate=73866.09/min [1720000], rate=73819.74/min [1730000], rate=73617.02/min [1740000], rate=73572.94/min [1750000], rate=73580.94/min [1760000], rate=73384.29/min [1770000], rate=73140.50/min [1780000], rate=73050.62/min [1790000], rate=73011.56/min [1800000], rate=73022.31/min [1810000], rate=73032.95/min [1820000], rate=73043.48/min [1830000], rate=73102.53/min [1840000], rate=73161.03/min [1850000], rate=73170.73/min [1860000], rate=73228.35/min [1870000], rate=73285.43/min [1880000], rate=73389.72/min [1890000], rate=73493.20/min [1900000], rate=73691.01/min [1910000], rate=74031.01/min [1920000], rate=74370.56/min [1930000], rate=74709.68/min [1940000], rate=75048.36/min [1950000], rate=75192.80/min [1960000], rate=75336.32/min [1970000], rate=75478.93/min [1980000], rate=75620.62/min [1990000], rate=75809.52/min [2000000], rate=75949.37/min [2010000], rate=75849.06/min [2020000], rate=75750.00/min [2030000], rate=75746.27/min [2040000], rate=75695.73/min [2050000], rate=75925.93/min [2060000], rate=75968.04/min [2070000], rate=75870.49/min [2080000], rate=75866.26/min [2090000], rate=75907.99/min [2100000], rate=75995.17/min [2110000], rate=76036.04/min [2120000], rate=76122.08/min [2130000], rate=76207.51/min [2140000], rate=76337.69/min [2150000], rate=76467.10/min [2160000], rate=76641.04/min [2170000], rate=76859.50/min [2180000], rate=77168.14/min [2190000], rate=77385.16/min [2200000], rate=77601.41/min [2210000], rate=77725.67/min [2220000], rate=77803.74/min [2230000], rate=77926.62/min [2240000], rate=78003.48/min [2250000], rate=78125.00/min [2260000], rate=78245.82/min -building interval tree based on /tmp/nxf.4mWoukv9HD/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=150000.00/min [30000], rate=128571.43/min [40000], rate=109090.91/min [50000], rate=107142.86/min [60000], rate=120000.00/min [70000], rate=135483.87/min [80000], rate=145454.55/min [90000], rate=150000.00/min [100000], rate=157894.74/min [110000], rate=173684.21/min [120000], rate=189473.68/min [130000], rate=205263.16/min [140000], rate=215384.62/min [150000], rate=209302.33/min [160000], rate=200000.00/min [170000], rate=200000.00/min [180000], rate=196363.64/min [190000], rate=190000.00/min [200000], rate=184615.38/min [210000], rate=172602.74/min [220000], rate=171428.57/min [230000], rate=179220.78/min [240000], rate=177777.78/min [250000], rate=178571.43/min [260000], rate=185714.29/min [270000], rate=184090.91/min [280000], rate=180645.16/min [290000], rate=183157.89/min [300000], rate=181818.18/min [310000], rate=184158.42/min [320000], rate=188235.29/min [330000], rate=192233.01/min [340000], rate=198058.25/min [350000], rate=203883.50/min [360000], rate=207692.31/min [370000], rate=213461.54/min [380000], rate=217142.86/min [390000], rate=214678.90/min [400000], rate=210526.32/min [410000], rate=208474.58/min [420000], rate=200000.00/min [430000], rate=195454.55/min [440000], rate=195555.56/min [450000], rate=197080.29/min [460000], rate=198561.15/min [470000], rate=201428.57/min [480000], rate=201398.60/min [490000], rate=204166.67/min [500000], rate=208333.33/min [510000], rate=211034.48/min [520000], rate=215172.41/min [530000], rate=216326.53/min [540000], rate=213157.89/min [550000], rate=211538.46/min [560000], rate=210000.00/min [570000], rate=208536.59/min [580000], rate=205917.16/min [590000], rate=202285.71/min [600000], rate=200000.00/min [610000], rate=202209.94/min [620000], rate=202173.91/min [630000], rate=203225.81/min [640000], rate=205347.59/min [650000], rate=204188.48/min [660000], rate=202040.82/min [670000], rate=203030.30/min [680000], rate=202985.07/min [690000], rate=203940.89/min [700000], rate=205882.35/min [710000], rate=207804.88/min [720000], rate=210731.71/min [730000], rate=213658.54/min [740000], rate=215533.98/min [750000], rate=218446.60/min [760000], rate=220289.86/min [770000], rate=220000.00/min [780000], rate=218691.59/min [790000], rate=218433.18/min [800000], rate=216216.22/min [810000], rate=212227.07/min [820000], rate=209361.70/min [830000], rate=210126.58/min [840000], rate=211764.71/min [850000], rate=212500.00/min [860000], rate=214107.88/min [870000], rate=213061.22/min [880000], rate=215510.20/min [890000], rate=217959.18/min [900000], rate=220408.16/min [910000], rate=221951.22/min [920000], rate=222580.65/min [930000], rate=221428.57/min [940000], rate=221176.47/min [950000], rate=221789.88/min [960000], rate=220689.66/min [970000], rate=217977.53/min [980000], rate=214598.54/min [990000], rate=214440.43/min [1000000], rate=215827.34/min [1010000], rate=215658.36/min [1020000], rate=215492.96/min [1030000], rate=216083.92/min [1040000], rate=215916.96/min [1050000], rate=215017.06/min [1060000], rate=214141.41/min [1070000], rate=214715.72/min [1080000], rate=216000.00/min [1090000], rate=215841.58/min [1100000], rate=214983.71/min [1110000], rate=214838.71/min [1120000], rate=214012.74/min [1130000], rate=211875.00/min [1140000], rate=209174.31/min [1150000], rate=207207.21/min [1160000], rate=208383.23/min [1170000], rate=209552.24/min [1180000], rate=210089.02/min [1190000], rate=210000.00/min [1200000], rate=210526.32/min [1210000], rate=212280.70/min [1220000], rate=214035.09/min [1230000], rate=215789.47/min [1240000], rate=216909.62/min [1250000], rate=216138.33/min [1260000], rate=215384.62/min [1270000], rate=215254.24/min [1280000], rate=215730.34/min [1290000], rate=213812.15/min [1300000], rate=211382.11/min [1310000], rate=210723.86/min [1320000], rate=211764.71/min [1330000], rate=211111.11/min [1340000], rate=211578.95/min [1350000], rate=212041.88/min [1360000], rate=211398.96/min [1370000], rate=210769.23/min [1380000], rate=210687.02/min [1390000], rate=211139.24/min [1400000], rate=212121.21/min [1410000], rate=205839.42/min [1420000], rate=186433.26/min [1430000], rate=174036.51/min [1440000], rate=162711.86/min [1450000], rate=153710.25/min [1460000], rate=146000.00/min [1470000], rate=139556.96/min [1480000], rate=133533.83/min [1490000], rate=126271.19/min [1500000], rate=121951.22/min [1510000], rate=118122.56/min [1520000], rate=115006.31/min [1530000], rate=111272.73/min [1540000], rate=108450.70/min [1550000], rate=105922.55/min [1560000], rate=103197.35/min [1570000], rate=100748.66/min [1580000], rate=98956.16/min [1590000], rate=97346.94/min [1600000], rate=96192.38/min [1610000], rate=95078.74/min [1620000], rate=94003.87/min [1630000], rate=92965.78/min [1640000], rate=92048.64/min [1650000], rate=91328.41/min [1660000], rate=90875.91/min [1670000], rate=90189.02/min [1680000], rate=89520.43/min [1690000], rate=88947.37/min [1700000], rate=88082.90/min [1710000], rate=87692.31/min [1720000], rate=86941.87/min [1730000], rate=86356.07/min [1740000], rate=85855.26/min [1750000], rate=85504.89/min [1760000], rate=85436.89/min [1770000], rate=85301.20/min [1780000], rate=85099.60/min [1790000], rate=85103.01/min [1800000], rate=85039.37/min [1810000], rate=85043.07/min [1820000], rate=85113.02/min [1830000], rate=85182.31/min [1840000], rate=85316.85/min [1850000], rate=85384.62/min [1860000], rate=85451.76/min [1870000], rate=85583.52/min [1880000], rate=85389.86/min [1890000], rate=85071.27/min [1900000], rate=84821.43/min [1910000], rate=84638.11/min [1920000], rate=84272.13/min [1930000], rate=84156.98/min [1940000], rate=84104.05/min [1950000], rate=84112.15/min [1960000], rate=84060.04/min [1970000], rate=83948.86/min [1980000], rate=83839.10/min [1990000], rate=83789.47/min [2000000], rate=83798.88/min [2010000], rate=83750.00/min [2020000], rate=83759.50/min [2030000], rate=83826.57/min [2040000], rate=83893.08/min [2050000], rate=84016.39/min [2060000], rate=84081.63/min [2070000], rate=84203.39/min [2080000], rate=84381.34/min [2090000], rate=84558.33/min [2100000], rate=83888.15/min [2110000], rate=83016.39/min [2120000], rate=82490.27/min [2130000], rate=82239.38/min [2140000], rate=81940.01/min [2150000], rate=81697.28/min [2160000], rate=81458.20/min [2170000], rate=81121.50/min [2180000], rate=80641.18/min [2190000], rate=80317.85/min [2200000], rate=79662.04/min [2210000], rate=79211.47/min [2220000], rate=78816.57/min [2230000], rate=78475.07/min [2240000], rate=78504.67/min [2250000], rate=78034.68/min [2260000], rate=77841.56/min -building interval tree based on /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=40000.00/min [20000], rate=41379.31/min [30000], rate=41860.47/min [40000], rate=40677.97/min [50000], rate=40540.54/min [60000], rate=40449.44/min [70000], rate=40384.62/min [80000], rate=40336.13/min [90000], rate=40298.51/min [100000], rate=41379.31/min [110000], rate=42307.69/min [120000], rate=43902.44/min [130000], rate=45614.04/min [140000], rate=47191.01/min [150000], rate=48913.04/min [160000], rate=50261.78/min [170000], rate=51515.15/min [180000], rate=52941.18/min [190000], rate=54285.71/min [200000], rate=52173.91/min [210000], rate=49802.37/min [220000], rate=48351.65/min [230000], rate=47422.68/min [240000], rate=46905.54/min [250000], rate=46728.97/min [260000], rate=46987.95/min [270000], rate=46551.72/min [280000], rate=46153.85/min [290000], rate=46031.75/min [300000], rate=45801.53/min [310000], rate=46039.60/min [320000], rate=46043.17/min [330000], rate=46261.68/min [340000], rate=46363.64/min [350000], rate=46770.60/min [360000], rate=47368.42/min [370000], rate=47844.83/min [380000], rate=48407.64/min [390000], rate=49056.60/min [400000], rate=49689.44/min [410000], rate=50409.84/min [420000], rate=51012.15/min [430000], rate=51600.00/min [440000], rate=52277.23/min [450000], rate=53149.61/min [460000], rate=53906.25/min [470000], rate=54440.15/min [480000], rate=54857.14/min [490000], rate=55367.23/min [500000], rate=55762.08/min [510000], rate=56250.00/min [520000], rate=56830.60/min [530000], rate=57400.72/min [540000], rate=58064.52/min [550000], rate=58718.86/min [560000], rate=59154.93/min [570000], rate=59067.36/min [580000], rate=58684.65/min [590000], rate=58803.99/min [600000], rate=58823.53/min [610000], rate=58653.85/min [620000], rate=58767.77/min [630000], rate=58970.36/min [640000], rate=59167.95/min [650000], rate=59360.73/min [660000], rate=59638.55/min [670000], rate=60000.00/min [680000], rate=60444.44/min [690000], rate=60882.35/min [700000], rate=61313.87/min [710000], rate=61649.78/min [720000], rate=62158.27/min [730000], rate=62840.75/min [740000], rate=63428.57/min [750000], rate=64102.56/min [760000], rate=64589.24/min [770000], rate=64345.40/min [780000], rate=64197.53/min [790000], rate=63967.61/min [800000], rate=63829.79/min [810000], rate=63612.57/min [820000], rate=63813.23/min [830000], rate=63764.40/min [840000], rate=63797.47/min [850000], rate=63829.79/min [860000], rate=64019.85/min [870000], rate=64364.98/min [880000], rate=64705.88/min [890000], rate=64884.57/min [900000], rate=65296.25/min [910000], rate=65625.00/min [920000], rate=65871.12/min [930000], rate=66192.17/min [940000], rate=66431.10/min [950000], rate=66822.98/min [960000], rate=66512.70/min [970000], rate=65466.82/min [980000], rate=64757.71/min [990000], rate=64146.87/min [1000000], rate=64239.83/min [1010000], rate=64536.74/min [1020000], rate=64899.26/min [1030000], rate=64779.87/min [1040000], rate=64197.53/min [1050000], rate=63765.18/min [1060000], rate=63600.00/min [1070000], rate=63501.48/min [1080000], rate=63219.51/min [1090000], rate=63188.41/min [1100000], rate=62857.14/min [1110000], rate=62593.98/min [1120000], rate=62164.66/min [1130000], rate=61692.45/min [1140000], rate=61510.79/min [1150000], rate=61333.33/min [1160000], rate=61052.63/min [1170000], rate=60726.64/min [1180000], rate=60306.64/min [1190000], rate=60101.01/min [1200000], rate=60050.04/min [1210000], rate=60049.63/min [1220000], rate=60098.52/min [1230000], rate=60000.00/min [1240000], rate=60000.00/min [1250000], rate=60144.35/min [1260000], rate=60000.00/min [1270000], rate=59952.79/min [1280000], rate=60000.00/min [1290000], rate=60093.17/min [1300000], rate=60231.66/min [1310000], rate=60229.89/min [1320000], rate=60319.88/min [1330000], rate=60408.78/min [1340000], rate=60405.71/min [1350000], rate=60492.91/min [1360000], rate=60579.06/min [1370000], rate=60664.21/min [1380000], rate=60748.35/min [1390000], rate=60875.91/min [1400000], rate=61002.18/min [1410000], rate=61171.37/min [1420000], rate=61383.29/min [1430000], rate=61593.68/min [1440000], rate=61802.58/min [1450000], rate=62054.21/min [1460000], rate=62304.41/min [1470000], rate=62508.86/min [1480000], rate=61881.53/min [1490000], rate=61401.10/min [1500000], rate=60893.10/min [1510000], rate=60480.64/min [1520000], rate=60237.78/min [1530000], rate=60000.00/min [1540000], rate=59728.51/min [1550000], rate=59539.05/min [1560000], rate=59428.57/min [1570000], rate=59282.57/min [1580000], rate=59324.16/min [1590000], rate=59328.36/min [1600000], rate=59332.51/min [1610000], rate=59227.47/min [1620000], rate=59268.29/min [1630000], rate=59200.97/min [1640000], rate=59241.42/min [1650000], rate=59316.96/min [1660000], rate=59391.77/min [1670000], rate=59430.60/min [1680000], rate=59469.03/min [1690000], rate=59332.94/min [1700000], rate=59096.18/min [1710000], rate=59169.55/min [1720000], rate=59276.28/min [1730000], rate=59382.15/min [1740000], rate=59487.18/min [1750000], rate=59625.21/min [1760000], rate=59762.31/min [1770000], rate=59932.28/min [1780000], rate=60135.14/min [1790000], rate=60303.20/min [1800000], rate=60470.32/min [1810000], rate=60602.68/min [1820000], rate=60700.39/min [1830000], rate=60932.30/min [1840000], rate=61197.34/min [1850000], rate=61495.84/min [1860000], rate=61759.82/min [1870000], rate=61954.72/min [1880000], rate=62114.54/min [1890000], rate=62273.48/min [1900000], rate=62431.54/min [1910000], rate=62588.75/min [1920000], rate=62676.82/min [1930000], rate=62224.61/min [1940000], rate=62046.91/min [1950000], rate=61872.03/min [1960000], rate=61602.93/min [1970000], rate=61402.60/min [1980000], rate=61205.56/min [1990000], rate=61042.94/min [2000000], rate=60882.80/min [2010000], rate=60694.51/min [2020000], rate=60751.88/min [2030000], rate=60869.57/min [2040000], rate=60744.42/min [2050000], rate=60680.81/min [2060000], rate=60677.47/min [2070000], rate=60614.93/min [2080000], rate=60523.76/min [2090000], rate=60433.73/min [2100000], rate=60373.74/min [2110000], rate=60400.76/min [2120000], rate=60427.55/min [2130000], rate=60425.53/min [2140000], rate=60451.98/min [2150000], rate=60534.96/min [2160000], rate=60617.40/min [2170000], rate=60699.30/min [2180000], rate=60780.67/min [2190000], rate=60861.51/min [2200000], rate=60941.83/min [2210000], rate=61021.63/min [2220000], rate=61128.96/min [2230000], rate=61207.69/min [2240000], rate=61313.87/min [2250000], rate=61419.47/min [2260000], rate=61552.43/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir --filt_file /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 6000000.00 reads per min processed... 12000000.00 reads per min processed... 9000000.00 reads per min processed... 12000000.00 reads per min processed... 10000000.00 reads per min processed... 12000000.00 reads per min processed... 10500000.00 reads per min processed... 12000000.00 reads per min processed... 10800000.00 reads per min processed... 10000000.00 reads per min processed... 11000000.00 reads per min processed... 10285714.29 reads per min processed... 11142857.14 reads per min processed... 9333333.33 reads per min processed... 9000000.00 reads per min processed... 8000000.00 reads per min processed... 7846153.85 reads per min processed... 7200000.00 reads per min processed... 7125000.00 reads per min processed... 7058823.53 reads per min processed... 6631578.95 reads per min processed... 6600000.00 reads per min processed... 6571428.57 reads per min processed... 6260869.57 reads per min processed... 6250000.00 reads per min processed... 6240000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 5800000.00 reads per min processed... 5625000.00 reads per min processed... 5636363.64 reads per min processed... 5485714.29 reads per min processed... 5500000.00 reads per min processed... 5368421.05 reads per min processed... 5250000.00 reads per min processed... 5400000.00 reads per min processed... 5285714.29 reads per min processed... 5302325.58 reads per min processed... 5318181.82 reads per min processed... 5217391.30 reads per min processed... 5234042.55 reads per min processed... 5250000.00 reads per min processed... 5265306.12 reads per min processed... 5176470.59 reads per min processed... 5192307.69 reads per min processed... 5307692.31 reads per min processed... 5320754.72 reads per min processed... 5433962.26 reads per min processed... 5444444.44 reads per min processed... 5555555.56 reads per min processed... 5563636.36 reads per min processed... 5672727.27 reads per min processed... 5678571.43 reads per min processed... 5684210.53 reads per min processed... 5789473.68 reads per min processed... 5793103.45 reads per min processed... 5896551.72 reads per min processed... 5800000.00 reads per min processed... 5803278.69 reads per min processed... 5714285.71 reads per min processed... 5718750.00 reads per min processed... 5723076.92 reads per min processed... 5727272.73 reads per min processed... 5647058.82 reads per min processed... 5652173.91 reads per min processed... 5657142.86 reads per min processed... 5661971.83 reads per min processed... 5666666.67 reads per min processed... 5594594.59 reads per min processed... 5600000.00 reads per min processed... 5532467.53 reads per min processed... 5538461.54 reads per min processed... 5475000.00 reads per min processed... 5481481.48 reads per min processed... 5487804.88 reads per min processed... 5493975.90 reads per min processed... 5435294.12 reads per min processed... 5441860.47 reads per min processed... 5448275.86 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.4mWoukv9HD/HeadNeckN_FFPE_L09_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.4mWoukv9HD/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -109071.612547 EM: Round [1] log likelihood: -108837.006408 EM: Round [2] log likelihood: -108741.603427 EM: Round [3] log likelihood: -108694.595865 EM: Round [4] log likelihood: -108669.340847 EM: Round [5] log likelihood: -108655.117904 EM: Round [6] log likelihood: -108646.794319 EM: Round [7] log likelihood: -108641.724424 EM: Round [8] log likelihood: -108638.503155 EM: Round [9] log likelihood: -108636.368866 EM: Round [10] log likelihood: -108634.898330 EM: Round [11] log likelihood: -108633.849040 EM: Round [12] log likelihood: -108633.077185 EM: Round [13] log likelihood: -108632.494397 EM: Round [14] log likelihood: -108632.044459 EM: Round [15] log likelihood: -108631.690414 EM: Round [16] log likelihood: -108631.407226 EM: Round [17] log likelihood: -108631.177475 EM: Round [18] log likelihood: -108630.988743 EM: Round [19] log likelihood: -108630.831994 EM: Round [20] log likelihood: -108630.700528 EM: Round [21] log likelihood: -108630.589298 EM: Round [22] log likelihood: -108630.494447 EM: Round [23] log likelihood: -108630.412986 EM: Round [24] log likelihood: -108630.342575 EM: Round [25] log likelihood: -108630.281361 EM: Round [26] log likelihood: -108630.227861 EM: Round [27] log likelihood: -108630.180878 EM: Round [28] log likelihood: -108630.139440 EM: Round [29] log likelihood: -108630.102746 EM: Round [30] log likelihood: -108630.070137 EM: Round [31] log likelihood: -108630.041062 EM: Round [32] log likelihood: -108630.015061 EM: Round [33] log likelihood: -108629.991745 EM: Round [34] log likelihood: -108629.970785 EM: Round [35] log likelihood: -108629.951900 EM: Round [36] log likelihood: -108629.934848 EM: Round [37] log likelihood: -108629.919423 EM: Round [38] log likelihood: -108629.905443 EM: Round [39] log likelihood: -108629.892754 EM: Round [40] log likelihood: -108629.881218 EM: Round [41] log likelihood: -108629.870717 EM: Round [42] log likelihood: -108629.861144 EM: Round [43] log likelihood: -108629.852408 EM: Round [44] log likelihood: -108629.844426 EM: Round [45] log likelihood: -108629.837126 EM: Round [46] log likelihood: -108629.830442 EM: Round [47] log likelihood: -108629.824317 EM: Round [48] log likelihood: -108629.818699 EM: Round [49] log likelihood: -108629.813542 EM: Round [50] log likelihood: -108629.808804 EM: Round [51] log likelihood: -108629.804448 EM: Round [52] log likelihood: -108629.800439 EM: Round [53] log likelihood: -108629.796748 EM: Round [54] log likelihood: -108629.793347 EM: Round [55] log likelihood: -108629.790211 EM: Round [56] log likelihood: -108629.787318 EM: Round [57] log likelihood: -108629.784647 EM: Round [58] log likelihood: -108629.782179 EM: Round [59] log likelihood: -108629.779897 EM: Round [60] log likelihood: -108629.777787 EM: Round [61] log likelihood: -108629.775834 EM: Round [62] log likelihood: -108629.774025 EM: Round [63] log likelihood: -108629.772348 EM: Round [64] log likelihood: -108629.770794 EM: Round [65] log likelihood: -108629.769351 EM: Round [66] log likelihood: -108629.768012 EM: Round [67] log likelihood: -108629.766769 EM: Round [68] log likelihood: -108629.765613 EM: Round [69] log likelihood: -108629.764537 EM: Round [70] log likelihood: -108629.763537 EM: Round [71] log likelihood: -108629.762605 EM: Round [72] log likelihood: -108629.761737 EM: Round [73] log likelihood: -108629.760928 EM: Round [74] log likelihood: -108629.760173 EM: Round [75] log likelihood: -108629.759468 EM: Round [76] log likelihood: -108629.758810 EM: Round [77] log likelihood: -108629.758195 EM: Round [78] log likelihood: -108629.757619 EM: Round [79] log likelihood: -108629.757081 EM: Round [80] log likelihood: -108629.756577 EM: Round [81] log likelihood: -108629.756105 EM: Round [82] log likelihood: -108629.755662 EM: Round [83] log likelihood: -108629.755246 EM: Round [84] log likelihood: -108629.754856 EM: Round [85] log likelihood: -108629.754490 EM: Round [86] log likelihood: -108629.754146 EM: Round [87] log likelihood: -108629.753822 EM: Round [88] log likelihood: -108629.753517 EM: Round [89] log likelihood: -108629.753230 EM: Round [90] log likelihood: -108629.752959 EM: Round [91] log likelihood: -108629.752704 EM: Round [92] log likelihood: -108629.752463 EM: Round [93] log likelihood: -108629.752235 EM: Round [94] log likelihood: -108629.752020 EM: Round [95] log likelihood: -108629.751817 EM: Round [96] log likelihood: -108629.751624 EM: Round [97] log likelihood: -108629.751442 EM: Round [98] log likelihood: -108629.751269 EM: Round [99] log likelihood: -108629.751106 EM: Round [100] log likelihood: -108629.750950 EM: Round [101] log likelihood: -108629.750803 EM: Round [102] log likelihood: -108629.750663 EM: Round [103] log likelihood: -108629.750529 EM: Round [104] log likelihood: -108629.750403 EM: Round [105] log likelihood: -108629.750282 EM: Round [106] log likelihood: -108629.750167 EM: Round [107] log likelihood: -108629.750058 EM: Round [108] log likelihood: -108629.749953 EM: Round [109] log likelihood: -108629.749853 EM: Stopping iterations at round 109 due to insufficient improvement in likelihood. EM: Starting log likelihood: -108982.461128 EM: Round [1] log likelihood: -108776.352360 EM: Round [2] log likelihood: -108696.914403 EM: Round [3] log likelihood: -108658.911162 EM: Round [4] log likelihood: -108638.869645 EM: Round [5] log likelihood: -108627.779123 EM: Round [6] log likelihood: -108621.416057 EM: Round [7] log likelihood: -108617.622505 EM: Round [8] log likelihood: -108615.262214 EM: Round [9] log likelihood: -108613.727159 EM: Round [10] log likelihood: -108612.685275 EM: Round [11] log likelihood: -108611.950089 EM: Round [12] log likelihood: -108611.413346 EM: Round [13] log likelihood: -108611.009895 EM: Round [14] log likelihood: -108610.699074 EM: Round [15] log likelihood: -108610.454593 EM: Round [16] log likelihood: -108610.258884 EM: Round [17] log likelihood: -108610.099849 EM: Round [18] log likelihood: -108609.968933 EM: Round [19] log likelihood: -108609.859945 EM: Round [20] log likelihood: -108609.768308 EM: Round [21] log likelihood: -108609.690581 EM: Round [22] log likelihood: -108609.624133 EM: Round [23] log likelihood: -108609.566928 EM: Round [24] log likelihood: -108609.517369 EM: Round [25] log likelihood: -108609.474189 EM: Round [26] log likelihood: -108609.436373 EM: Round [27] log likelihood: -108609.403101 EM: Round [28] log likelihood: -108609.373703 EM: Round [29] log likelihood: -108609.347630 EM: Round [30] log likelihood: -108609.324424 EM: Round [31] log likelihood: -108609.303707 EM: Round [32] log likelihood: -108609.285157 EM: Round [33] log likelihood: -108609.268506 EM: Round [34] log likelihood: -108609.253524 EM: Round [35] log likelihood: -108609.240014 EM: Round [36] log likelihood: -108609.227808 EM: Round [37] log likelihood: -108609.216759 EM: Round [38] log likelihood: -108609.206742 EM: Round [39] log likelihood: -108609.197647 EM: Round [40] log likelihood: -108609.189376 EM: Round [41] log likelihood: -108609.181846 EM: Round [42] log likelihood: -108609.174981 EM: Round [43] log likelihood: -108609.168716 EM: Round [44] log likelihood: -108609.162993 EM: Round [45] log likelihood: -108609.157759 EM: Round [46] log likelihood: -108609.152969 EM: Round [47] log likelihood: -108609.148580 EM: Round [48] log likelihood: -108609.144556 EM: Round [49] log likelihood: -108609.140864 EM: Round [50] log likelihood: -108609.137473 EM: Round [51] log likelihood: -108609.134357 EM: Round [52] log likelihood: -108609.131491 EM: Round [53] log likelihood: -108609.128854 EM: Round [54] log likelihood: -108609.126426 EM: Round [55] log likelihood: -108609.124188 EM: Round [56] log likelihood: -108609.122125 EM: Round [57] log likelihood: -108609.120222 EM: Round [58] log likelihood: -108609.118465 EM: Round [59] log likelihood: -108609.116842 EM: Round [60] log likelihood: -108609.115342 EM: Round [61] log likelihood: -108609.113955 EM: Round [62] log likelihood: -108609.112671 EM: Round [63] log likelihood: -108609.111482 EM: Round [64] log likelihood: -108609.110382 EM: Round [65] log likelihood: -108609.109361 EM: Round [66] log likelihood: -108609.108415 EM: Round [67] log likelihood: -108609.107536 EM: Round [68] log likelihood: -108609.106721 EM: Round [69] log likelihood: -108609.105963 EM: Round [70] log likelihood: -108609.105259 EM: Round [71] log likelihood: -108609.104603 EM: Round [72] log likelihood: -108609.103994 EM: Round [73] log likelihood: -108609.103426 EM: Round [74] log likelihood: -108609.102897 EM: Round [75] log likelihood: -108609.102403 EM: Round [76] log likelihood: -108609.101943 EM: Round [77] log likelihood: -108609.101513 EM: Round [78] log likelihood: -108609.101112 EM: Round [79] log likelihood: -108609.100737 EM: Round [80] log likelihood: -108609.100386 EM: Round [81] log likelihood: -108609.100057 EM: Round [82] log likelihood: -108609.099750 EM: Round [83] log likelihood: -108609.099462 EM: Round [84] log likelihood: -108609.099191 EM: Round [85] log likelihood: -108609.098938 EM: Round [86] log likelihood: -108609.098700 EM: Round [87] log likelihood: -108609.098476 EM: Round [88] log likelihood: -108609.098265 EM: Round [89] log likelihood: -108609.098068 EM: Round [90] log likelihood: -108609.097881 EM: Round [91] log likelihood: -108609.097706 EM: Round [92] log likelihood: -108609.097540 EM: Round [93] log likelihood: -108609.097384 EM: Round [94] log likelihood: -108609.097236 EM: Round [95] log likelihood: -108609.097097 EM: Round [96] log likelihood: -108609.096965 EM: Round [97] log likelihood: -108609.096841 EM: Round [98] log likelihood: -108609.096723 EM: Round [99] log likelihood: -108609.096611 EM: Round [100] log likelihood: -108609.096505 EM: Round [101] log likelihood: -108609.096405 EM: Round [102] log likelihood: -108609.096309 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.4mWoukv9HD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.4mWoukv9HD/./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.4mWoukv9HD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.4mWoukv9HD/./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.4mWoukv9HD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 138319193 > /tmp/nxf.4mWoukv9HD/./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.4mWoukv9HD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir > /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir --annotate /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.4mWoukv9HD/./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.4mWoukv9HD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir -done, see /tmp/nxf.4mWoukv9HD/./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.4mWoukv9HD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.4mWoukv9HD/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 597, filtered: 5565) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.4mWoukv9HD/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.4mWoukv9HD/./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.4mWoukv9HD/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 [ENSG00000282890.1] WARNING, no entry stored in dbm for [ENSG00000068781.21] WARNING, no entry stored in dbm for [ENSG00000242207.1] WARNING, no entry stored in dbm for [ENSG00000286511.1] WARNING, no entry stored in dbm for [ENSG00000229739.4] WARNING, no entry stored in dbm for [ENSG00000237491.10] WARNING, no entry stored in dbm for [ENSG00000227733.10] WARNING, no entry stored in dbm for [ENSG00000225465.10] WARNING, no entry stored in dbm for [ENSG00000214433.4] WARNING, no entry stored in dbm for [ENSG00000220685.3] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000288663.1] WARNING, no entry stored in dbm for [ENSG00000275223.1] WARNING, no entry stored in dbm for [ENSG00000237004.4] WARNING, no entry stored in dbm for [ENSG00000224505.2] WARNING, no entry stored in dbm for [ENSG00000234420.7] WARNING, no entry stored in dbm for [ENSG00000280414.1] WARNING, no entry stored in dbm for [ENSG00000231559.1] WARNING, no entry stored in dbm for [ENSG00000203993.6] WARNING, no entry stored in dbm for [ENSG00000254584.2] WARNING, no entry stored in dbm for [ENSG00000229036.7] WARNING, no entry stored in dbm for [ENSG00000256925.3] WARNING, no entry stored in dbm for [ENSG00000214049.8] WARNING, no entry stored in dbm for [ENSG00000286681.1] WARNING, no entry stored in dbm for [ENSG00000278591.1] WARNING, no entry stored in dbm for [ENSG00000275219.1] WARNING, no entry stored in dbm for [ENSG00000274452.1] WARNING, no entry stored in dbm for [ENSG00000274062.1] WARNING, no entry stored in dbm for [ENSG00000274862.1] WARNING, no entry stored in dbm for [ENSG00000278774.1] WARNING, no entry stored in dbm for [ENSG00000277903.1] WARNING, no entry stored in dbm for [ENSG00000276596.1] WARNING, no entry stored in dbm for [ENSG00000278048.1] WARNING, no entry stored in dbm for [ENSG00000274432.1] WARNING, no entry stored in dbm for [ENSG00000273709.1] WARNING, no entry stored in dbm for [ENSG00000275616.1] WARNING, no entry stored in dbm for [ENSG00000253232.1] WARNING, no entry stored in dbm for [ENSG00000236786.1] 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 [ENSG00000287243.2] WARNING, no entry stored in dbm for [ENSG00000287593.1] WARNING, no entry stored in dbm for [ENSG00000253894.2] WARNING, no entry stored in dbm for [ENSG00000274259.2] WARNING, no entry stored in dbm for [ENSG00000234638.1] WARNING, no entry stored in dbm for [ENSG00000240350.3] WARNING, no entry stored in dbm for [ENSG00000286953.1] WARNING, no entry stored in dbm for [ENSG00000248551.1] WARNING, no entry stored in dbm for [ENSG00000280414.1] WARNING, no entry stored in dbm for [ENSG00000213332.4] WARNING, no entry stored in dbm for [ENSG00000224281.5] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000242798.1] WARNING, no entry stored in dbm for [ENSG00000261711.6] WARNING, no entry stored in dbm for [ENSG00000196183.5] WARNING, no entry stored in dbm for [ENSG00000229865.1] WARNING, no entry stored in dbm for [ENSG00000235670.1] WARNING, no entry stored in dbm for [ENSG00000241423.2] WARNING, no entry stored in dbm for [ENSG00000274585.1] WARNING, no entry stored in dbm for [ENSG00000272655.2] WARNING, no entry stored in dbm for [ENSG00000201059.1] WARNING, no entry stored in dbm for [ENSG00000199415.1] WARNING, no entry stored in dbm for [ENSG00000201059.1] WARNING, no entry stored in dbm for [ENSG00000199839.1] WARNING, no entry stored in dbm for [ENSG00000201059.1] WARNING, no entry stored in dbm for [ENSG00000201413.1] WARNING, no entry stored in dbm for [ENSG00000239899.3] WARNING, no entry stored in dbm for [ENSG00000241175.3] WARNING, no entry stored in dbm for [ENSG00000264833.1] WARNING, no entry stored in dbm for [ENSG00000239868.3] WARNING, no entry stored in dbm for [ENSG00000239437.3] WARNING, no entry stored in dbm for [ENSG00000239868.3] WARNING, no entry stored in dbm for [ENSG00000263968.2] WARNING, no entry stored in dbm for [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000201901.1] WARNING, no entry stored in dbm for [ENSG00000201901.1] WARNING, no entry 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no entry stored in dbm for [ENSG00000287576.1] 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 [ENSG00000223117.1] WARNING, no entry stored in dbm for [ENSG00000222979.1] WARNING, no entry stored in dbm for [ENSG00000199683.1] WARNING, no entry stored in dbm for [ENSG00000201901.1] WARNING, no entry stored in dbm for [ENSG00000228714.4] WARNING, no entry stored in dbm for [ENSG00000239636.1] WARNING, no entry stored in dbm for [ENSG00000183292.13] WARNING, no entry stored in dbm for [ENSG00000231609.7] WARNING, no entry stored in dbm for [ENSG00000240498.9] WARNING, no entry stored in dbm for [ENSG00000239556.4] WARNING, no entry stored in dbm for [ENSG00000270344.3] WARNING, no entry stored in dbm for [ENSG00000244257.5] WARNING, no entry stored in dbm for [ENSG00000154898.15] WARNING, no entry stored in dbm for [ENSG00000236229.1] WARNING, no entry stored in dbm for [ENSG00000233223.3] WARNING, no entry stored in dbm for [ENSG00000264116.6] WARNING, no entry stored in dbm for [ENSG00000223482.8] WARNING, no entry stored in dbm for [ENSG00000259884.1] WARNING, no entry stored in dbm for [ENSG00000183604.14] WARNING, no entry stored in dbm for [ENSG00000249448.1] WARNING, no entry stored in dbm for [ENSG00000236051.7] WARNING, no entry stored in dbm for [ENSG00000236051.7] WARNING, no entry stored in dbm for [ENSG00000215866.8] WARNING, no entry stored in dbm for [ENSG00000237238.3] WARNING, no entry stored in dbm for [ENSG00000225783.8] WARNING, no entry stored in dbm for [ENSG00000180747.15] WARNING, no entry stored in dbm for [ENSG00000186056.10] WARNING, no entry stored in dbm for [ENSG00000253320.7] WARNING, no entry stored in dbm for [ENSG00000258100.3] WARNING, no entry stored in dbm for [ENSG00000227082.3] WARNING, no entry stored in dbm for [ENSG00000286293.1] WARNING, no entry stored in dbm for [ENSG00000255008.3] WARNING, no entry stored in dbm for [ENSG00000263146.2] WARNING, no entry stored in dbm for [ENSG00000287356.1] WARNING, no entry stored in dbm for [ENSG00000220804.8] WARNING, no entry stored in dbm for [ENSG00000281896.1] WARNING, no entry stored in dbm for [ENSG00000225269.3] WARNING, no entry stored in dbm for [ENSG00000232677.9] WARNING, no entry stored in dbm for [ENSG00000241469.9] WARNING, no entry stored in dbm for [ENSG00000227674.3] WARNING, no entry stored in dbm for [ENSG00000188185.13] WARNING, no entry stored in dbm for [ENSG00000229205.5] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000226806.1] WARNING, no entry stored in dbm for [ENSG00000240668.1] WARNING, no entry stored in dbm for [ENSG00000252827.1] WARNING, no entry stored in dbm for [ENSG00000258548.6] WARNING, no entry stored in dbm for [ENSG00000229191.1] WARNING, no entry stored in dbm for [ENSG00000214922.9] WARNING, no entry stored in dbm for [ENSG00000244627.5] WARNING, no entry stored in 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stored in dbm for [ENSG00000283541.1] WARNING, no entry stored in dbm for [ENSG00000267506.5] WARNING, no entry stored in dbm for [ENSG00000224329.2] WARNING, no entry stored in dbm for [ENSG00000277576.1] WARNING, no entry stored in dbm for [ENSG00000280254.1] WARNING, no entry stored in dbm for [ENSG00000224086.6] WARNING, no entry stored in dbm for [ENSG00000268001.1] WARNING, no entry stored in dbm for [ENSG00000186312.10] WARNING, no entry stored in dbm for [ENSG00000178722.13] WARNING, no entry stored in dbm for [ENSG00000224750.6] WARNING, no entry stored in dbm for [ENSG00000274525.1] WARNING, no entry stored in dbm for [ENSG00000158482.10] WARNING, no entry stored in dbm for [ENSG00000230804.2] WARNING, no entry stored in dbm for [ENSG00000236114.1] WARNING, no entry stored in dbm for [ENSG00000287666.1] WARNING, no entry stored in dbm for [ENSG00000177946.7] WARNING, no entry stored in dbm for [ENSG00000235138.1] WARNING, no entry stored in dbm for [ENSG00000287991.1] WARNING, no entry stored in dbm for [ENSG00000279609.1] WARNING, no entry stored in dbm for [ENSG00000271989.1] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000227220.1] WARNING, no entry stored in dbm for [ENSG00000236166.1] WARNING, no entry stored in dbm for [ENSG00000227486.2] WARNING, no entry stored in dbm for [ENSG00000271746.1] WARNING, no entry stored in dbm for [ENSG00000215022.7] WARNING, no entry stored in dbm for [ENSG00000199773.1] WARNING, no entry stored in dbm for [ENSG00000286729.1] WARNING, no entry stored in dbm for [ENSG00000233597.3] WARNING, no entry stored in dbm for [ENSG00000232172.1] WARNING, no entry stored in dbm for [ENSG00000251408.1] WARNING, no entry stored in dbm for [ENSG00000282375.1] WARNING, no entry stored in dbm for [ENSG00000231252.3] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000249149.2] WARNING, no entry stored in dbm for [ENSG00000286152.1] WARNING, no entry stored in dbm for [ENSG00000283674.3] WARNING, no entry stored in dbm for [ENSG00000235027.1] WARNING, no entry stored in dbm for [ENSG00000287576.1] WARNING, no entry stored in dbm for [ENSG00000201901.1] WARNING, no entry stored in dbm for [ENSG00000185641.6] WARNING, no entry stored in dbm for [ENSG00000257817.2] WARNING, no entry stored in dbm for [ENSG00000205682.2] WARNING, no entry stored in dbm for [ENSG00000213963.6] WARNING, no entry stored in dbm for [ENSG00000285582.1] WARNING, no entry stored in dbm for [ENSG00000261526.2] WARNING, no entry stored in dbm for [ENSG00000268049.1] WARNING, no entry stored in dbm for [ENSG00000272180.1] WARNING, no entry stored in dbm for [ENSG00000225840.2] WARNING, no entry stored in dbm for [ENSG00000282890.1] WARNING, no entry stored in dbm for [ENSG00000068781.21] WARNING, no entry stored in dbm for [ENSG00000279142.1] WARNING, no entry stored in dbm for [ENSG00000176593.8] WARNING, no entry stored in dbm for [ENSG00000257403.2] WARNING, no entry stored in dbm for [ENSG00000189149.12] WARNING, no entry stored in dbm for [ENSG00000226472.8] WARNING, no entry stored in dbm for [ENSG00000262292.2] WARNING, no entry stored in dbm for [ENSG00000235852.1] WARNING, no entry stored in dbm for [ENSG00000274712.2] WARNING, no entry stored in dbm for [ENSG00000274712.2] WARNING, no entry stored in dbm for [ENSG00000274712.2] WARNING, no entry stored in dbm for [ENSG00000274712.2] WARNING, no entry stored in dbm for [ENSG00000230305.2] WARNING, no entry stored in dbm for [ENSG00000239556.4] WARNING, no entry stored in dbm for [ENSG00000226592.1] WARNING, no entry stored in dbm for [ENSG00000239791.2] * STAR-Fusion complete. See output: /tmp/nxf.4mWoukv9HD/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)