Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/ac0c2247a158632caaf9371c0f5aa7/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2_2.fastp.fastq.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/4e1305784bf08ced137a6cd7381508/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/4e1305784bf08ced137a6cd7381508/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/5ee001e18e359b1d323646a1b56d82/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/ac0c2247a158632caaf9371c0f5aa7/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2_1.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.nhLzySAF68/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.nhLzySAF68/./star-fusion.preliminary -sample contains 106860155 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir -J /tmp/nxf.nhLzySAF68/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Chimeric.out.junction -O /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.nhLzySAF68/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Chimeric.out.junction -building interval tree based on /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=46153.85/min [20000], rate=52173.91/min [30000], rate=47368.42/min [40000], rate=45283.02/min [50000], rate=46153.85/min [60000], rate=49315.07/min [70000], rate=50602.41/min [80000], rate=52747.25/min [90000], rate=54545.45/min [100000], rate=53571.43/min [110000], rate=52800.00/min [120000], rate=52941.18/min [130000], rate=53424.66/min [140000], rate=53164.56/min [150000], rate=53892.22/min [160000], rate=54857.14/min [170000], rate=56353.59/min [180000], rate=58695.65/min [190000], rate=60962.57/min [200000], rate=61855.67/min [210000], rate=62376.24/min [220000], rate=62559.24/min [230000], rate=63302.75/min [240000], rate=64000.00/min [250000], rate=64377.68/min [260000], rate=65000.00/min [270000], rate=66122.45/min [280000], rate=66932.27/min [290000], rate=67181.47/min [300000], rate=65454.55/min [310000], rate=64583.33/min [320000], rate=64214.05/min [330000], rate=64077.67/min [340000], rate=63157.89/min [350000], rate=63636.36/min [360000], rate=63716.81/min [370000], rate=63793.10/min [380000], rate=63865.55/min [390000], rate=63934.43/min [400000], rate=64516.13/min [410000], rate=64397.91/min [420000], rate=64450.13/min [430000], rate=64824.12/min [440000], rate=64705.88/min [450000], rate=64133.02/min [460000], rate=65094.34/min [470000], rate=66197.18/min [480000], rate=67289.72/min [490000], rate=68531.47/min [500000], rate=69767.44/min [510000], rate=71162.79/min [520000], rate=72389.79/min [530000], rate=73441.11/min [540000], rate=74311.93/min [550000], rate=74829.93/min [560000], rate=76018.10/min [570000], rate=76339.29/min [580000], rate=76315.79/min [590000], rate=76789.59/min [600000], rate=77419.35/min [610000], rate=77215.19/min [620000], rate=77338.88/min [630000], rate=77777.78/min [640000], rate=78207.74/min [650000], rate=78000.00/min [660000], rate=77495.11/min [670000], rate=78058.25/min [680000], rate=78764.48/min [690000], rate=79615.38/min [700000], rate=80000.00/min [710000], rate=79924.95/min [720000], rate=79266.06/min [730000], rate=78918.92/min [740000], rate=78031.63/min [750000], rate=77586.21/min [760000], rate=77815.70/min [770000], rate=77908.94/min [780000], rate=78130.22/min [790000], rate=77960.53/min [800000], rate=78175.90/min [810000], rate=78768.23/min [820000], rate=77725.12/min [830000], rate=77934.27/min [840000], rate=77538.46/min [850000], rate=77272.73/min [860000], rate=77945.62/min [870000], rate=78733.03/min [880000], rate=79398.50/min [890000], rate=80180.18/min [900000], rate=80959.52/min [910000], rate=81859.07/min [920000], rate=82511.21/min [930000], rate=83159.46/min [940000], rate=83308.71/min [950000], rate=83946.98/min [960000], rate=84087.59/min [970000], rate=83741.01/min [980000], rate=83880.17/min [990000], rate=84375.00/min [1000000], rate=83682.01/min [1010000], rate=83701.66/min [1020000], rate=84181.57/min [1030000], rate=84311.05/min [1040000], rate=83983.85/min [1050000], rate=84000.00/min [1060000], rate=84015.85/min [1070000], rate=84473.68/min [1080000], rate=85039.37/min [1090000], rate=85602.09/min [1100000], rate=86274.51/min [1110000], rate=86945.17/min [1120000], rate=87614.08/min [1130000], rate=88281.25/min [1140000], rate=88946.68/min [1150000], rate=89494.16/min [1160000], rate=90272.37/min [1170000], rate=90815.01/min [1180000], rate=91472.87/min [1190000], rate=91655.97/min [1200000], rate=91370.56/min [1210000], rate=90977.44/min [1220000], rate=90594.06/min [1230000], rate=90000.00/min [1240000], rate=89963.72/min [1250000], rate=89928.06/min [1260000], rate=90107.27/min [1270000], rate=89964.58/min [1280000], rate=89510.49/min [1290000], rate=89583.33/min [1300000], rate=89347.08/min [1310000], rate=89014.72/min [1320000], rate=88000.00/min [1330000], rate=86739.13/min [1340000], rate=86918.92/min [1350000], rate=87190.53/min [1360000], rate=87179.49/min [1370000], rate=87446.81/min [1380000], rate=87249.74/min [1390000], rate=87421.38/min [1400000], rate=87046.63/min [1410000], rate=87306.50/min [1420000], rate=87654.32/min [1430000], rate=88180.88/min [1440000], rate=88343.56/min [1450000], rate=88414.63/min [1460000], rate=88306.45/min [1470000], rate=88200.00/min [1480000], rate=88182.72/min [1490000], rate=88165.68/min [1500000], rate=88235.29/min [1510000], rate=88476.56/min [1520000], rate=88543.69/min [1530000], rate=87846.89/min [1540000], rate=87334.59/min [1550000], rate=86834.73/min [1560000], rate=86426.59/min [1570000], rate=86342.80/min [1580000], rate=85869.57/min [1590000], rate=85714.29/min [1600000], rate=85485.31/min [1610000], rate=85260.37/min [1620000], rate=85113.84/min [1630000], rate=85191.64/min [1640000], rate=85121.11/min [1650000], rate=83827.27/min [1660000], rate=82518.64/min [1670000], rate=81529.70/min [1680000], rate=80511.18/min [1690000], rate=79716.98/min [1700000], rate=78825.35/min [1710000], rate=78320.61/min [1720000], rate=77072.44/min [1730000], rate=75988.29/min [1740000], rate=75161.99/min [1750000], rate=74733.10/min [1760000], rate=74471.09/min [1770000], rate=74369.75/min [1780000], rate=74166.67/min [1790000], rate=73865.20/min [1800000], rate=73720.14/min [1810000], rate=73279.35/min [1820000], rate=73141.33/min [1830000], rate=73005.32/min [1840000], rate=72823.22/min [1850000], rate=72786.89/min [1860000], rate=72750.98/min [1870000], rate=72904.48/min [1880000], rate=73199.22/min [1890000], rate=73303.17/min [1900000], rate=73311.90/min [1910000], rate=73414.48/min [1920000], rate=73096.45/min [1930000], rate=72465.58/min [1940000], rate=72074.30/min [1950000], rate=71735.13/min [1960000], rate=71489.36/min [1970000], rate=71333.74/min [1980000], rate=71095.15/min [1990000], rate=70860.53/min [2000000], rate=70754.72/min [2010000], rate=70650.26/min [2020000], rate=70506.11/min [2030000], rate=70526.93/min [2040000], rate=70628.97/min [2050000], rate=70649.05/min [2060000], rate=70709.38/min [2070000], rate=70688.67/min [2080000], rate=70389.17/min [2090000], rate=69899.67/min [2100000], rate=69498.07/min [2110000], rate=69180.33/min [2120000], rate=68943.09/min [2130000], rate=68746.64/min -building interval tree based on /tmp/nxf.nhLzySAF68/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=42857.14/min [30000], rate=45000.00/min [40000], rate=44444.44/min [50000], rate=44776.12/min [60000], rate=46753.25/min [70000], rate=46153.85/min [80000], rate=47524.75/min [90000], rate=48648.65/min [100000], rate=49586.78/min [110000], rate=51562.50/min [120000], rate=53333.33/min [130000], rate=54929.58/min [140000], rate=56375.84/min [150000], rate=59602.65/min [160000], rate=58895.71/min [170000], rate=55135.14/min [180000], rate=52427.18/min [190000], rate=50666.67/min [200000], rate=50000.00/min [210000], rate=49027.24/min [220000], rate=47653.43/min [230000], rate=46779.66/min [240000], rate=45283.02/min [250000], rate=44117.65/min [260000], rate=43575.42/min [270000], rate=43665.77/min [280000], rate=43864.23/min [290000], rate=43500.00/min [300000], rate=43583.54/min [310000], rate=43764.71/min [320000], rate=44036.70/min [330000], rate=44394.62/min [340000], rate=44541.48/min [350000], rate=45064.38/min [360000], rate=46153.85/min [370000], rate=47234.04/min [380000], rate=48000.00/min [390000], rate=48247.42/min [400000], rate=48681.54/min [410000], rate=49200.00/min [420000], rate=49704.14/min [430000], rate=50292.40/min [440000], rate=50190.11/min [450000], rate=49180.33/min [460000], rate=48251.75/min [470000], rate=47000.00/min [480000], rate=46302.25/min [490000], rate=46592.71/min [500000], rate=46082.95/min [510000], rate=45808.38/min [520000], rate=45481.05/min [530000], rate=45624.10/min [540000], rate=45633.80/min [550000], rate=45643.15/min [560000], rate=45528.46/min [570000], rate=45358.09/min [580000], rate=45253.58/min [590000], rate=45095.54/min [600000], rate=45000.00/min [610000], rate=44743.28/min [620000], rate=44338.50/min [630000], rate=44680.85/min [640000], rate=44912.28/min [650000], rate=44982.70/min [660000], rate=45308.92/min [670000], rate=45629.97/min [680000], rate=45997.75/min [690000], rate=46051.17/min [700000], rate=46255.51/min [710000], rate=46506.55/min [720000], rate=46702.70/min [730000], rate=46995.71/min [740000], rate=47133.76/min [750000], rate=47518.48/min [760000], rate=47648.90/min [770000], rate=47925.31/min [780000], rate=48247.42/min [790000], rate=48318.04/min [800000], rate=48435.92/min [810000], rate=48551.45/min [820000], rate=48857.99/min [830000], rate=49015.75/min [840000], rate=48979.59/min [850000], rate=49132.95/min [860000], rate=49283.67/min [870000], rate=49338.37/min [880000], rate=49162.01/min [890000], rate=49398.70/min [900000], rate=49450.55/min [910000], rate=49546.28/min [920000], rate=49819.49/min [930000], rate=50000.00/min [940000], rate=50088.81/min [950000], rate=50131.93/min [960000], rate=50043.44/min [970000], rate=50302.51/min [980000], rate=50299.40/min [990000], rate=50424.45/min [1000000], rate=50675.68/min [1010000], rate=50711.30/min [1020000], rate=50746.27/min [1030000], rate=50738.92/min [1040000], rate=50855.75/min [1050000], rate=50888.53/min [1060000], rate=50798.72/min [1070000], rate=50871.63/min [1080000], rate=50983.48/min [1090000], rate=50815.85/min [1100000], rate=50965.25/min [1110000], rate=51034.48/min [1120000], rate=51102.66/min [1130000], rate=51285.93/min [1140000], rate=51428.57/min [1150000], rate=51569.51/min [1160000], rate=51670.38/min [1170000], rate=51808.12/min [1180000], rate=51830.16/min [1190000], rate=51889.53/min [1200000], rate=51948.05/min [1210000], rate=51894.21/min [1220000], rate=51878.10/min [1230000], rate=51935.26/min [1240000], rate=51991.61/min [1250000], rate=52047.19/min [1260000], rate=52246.03/min [1270000], rate=52407.15/min [1280000], rate=52638.79/min [1290000], rate=52796.73/min [1300000], rate=53025.15/min [1310000], rate=53072.25/min [1320000], rate=52905.81/min [1330000], rate=52777.78/min [1340000], rate=52721.31/min [1350000], rate=52563.27/min [1360000], rate=52442.16/min [1370000], rate=52456.92/min [1380000], rate=52471.48/min [1390000], rate=52485.84/min [1400000], rate=52532.83/min [1410000], rate=52677.46/min [1420000], rate=52755.42/min [1430000], rate=52897.66/min [1440000], rate=53038.67/min [1450000], rate=53308.82/min [1460000], rate=53479.85/min [1470000], rate=53682.29/min [1480000], rate=53948.97/min [1490000], rate=54083.48/min [1500000], rate=54315.03/min [1510000], rate=54545.45/min [1520000], rate=54741.90/min [1530000], rate=54871.49/min [1540000], rate=55000.00/min [1550000], rate=55127.45/min [1560000], rate=55026.46/min [1570000], rate=54863.13/min [1580000], rate=54797.69/min [1590000], rate=54701.83/min [1600000], rate=54483.54/min [1610000], rate=54483.93/min [1620000], rate=54545.45/min [1630000], rate=54484.68/min [1640000], rate=54364.64/min [1650000], rate=54306.09/min [1660000], rate=54366.81/min [1670000], rate=54367.88/min [1680000], rate=54310.34/min [1690000], rate=54311.73/min [1700000], rate=54400.00/min [1710000], rate=54429.71/min [1720000], rate=54661.02/min [1730000], rate=54949.71/min [1740000], rate=55267.34/min [1750000], rate=55555.56/min [1760000], rate=55813.95/min [1770000], rate=56101.43/min [1780000], rate=56388.60/min [1790000], rate=56585.88/min [1800000], rate=56663.17/min [1810000], rate=56769.47/min [1820000], rate=56815.82/min [1830000], rate=56891.19/min [1840000], rate=57024.79/min [1850000], rate=56923.08/min [1860000], rate=56880.73/min [1870000], rate=56925.42/min [1880000], rate=56940.94/min [1890000], rate=57186.08/min [1900000], rate=57401.81/min [1910000], rate=57443.61/min [1920000], rate=57399.10/min [1930000], rate=57298.37/min [1940000], rate=57368.16/min [1950000], rate=57437.41/min [1960000], rate=57478.01/min [1970000], rate=57574.28/min [1980000], rate=57669.90/min [1990000], rate=57820.82/min [2000000], rate=57943.02/min [2010000], rate=58120.48/min [2020000], rate=58325.31/min [2030000], rate=58585.86/min [2040000], rate=58817.88/min [2050000], rate=59021.11/min [2060000], rate=59195.40/min [2070000], rate=59369.02/min [2080000], rate=59456.88/min [2090000], rate=59572.45/min [2100000], rate=59743.95/min [2110000], rate=59886.47/min -building interval tree based on /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=100000.00/min [30000], rate=81818.18/min [40000], rate=80000.00/min [50000], rate=90909.09/min [60000], rate=92307.69/min [70000], rate=105000.00/min [80000], rate=104347.83/min [90000], rate=98181.82/min [100000], rate=98360.66/min [110000], rate=100000.00/min [120000], rate=100000.00/min [130000], rate=100000.00/min [140000], rate=96551.72/min [150000], rate=102272.73/min [160000], rate=105494.51/min [170000], rate=107368.42/min [180000], rate=110204.08/min [190000], rate=109615.38/min [200000], rate=110091.74/min [210000], rate=109565.22/min [220000], rate=112820.51/min [230000], rate=115966.39/min [240000], rate=120000.00/min [250000], rate=123966.94/min [260000], rate=128925.62/min [270000], rate=133884.30/min [280000], rate=138842.98/min [290000], rate=142622.95/min [300000], rate=146341.46/min [310000], rate=150000.00/min [320000], rate=154838.71/min [330000], rate=155905.51/min [340000], rate=154545.45/min [350000], rate=151079.14/min [360000], rate=148965.52/min [370000], rate=145098.04/min [380000], rate=142500.00/min [390000], rate=143558.28/min [400000], rate=143712.57/min [410000], rate=144705.88/min [420000], rate=144000.00/min [430000], rate=143333.33/min [440000], rate=142702.70/min [450000], rate=142857.14/min [460000], rate=141538.46/min [470000], rate=140298.51/min [480000], rate=139805.83/min [490000], rate=142718.45/min [500000], rate=142180.09/min [510000], rate=142990.65/min [520000], rate=141818.18/min [530000], rate=141333.33/min [540000], rate=140869.57/min [550000], rate=141630.90/min [560000], rate=142978.72/min [570000], rate=144915.25/min [580000], rate=146835.44/min [590000], rate=149367.09/min [600000], rate=151898.73/min [610000], rate=154430.38/min [620000], rate=156302.52/min [630000], rate=158159.00/min [640000], rate=160669.46/min [650000], rate=162500.00/min [660000], rate=164315.35/min [670000], rate=161445.78/min [680000], rate=159375.00/min [690000], rate=158015.27/min [700000], rate=156133.83/min [710000], rate=154347.83/min [720000], rate=154285.71/min [730000], rate=154225.35/min [740000], rate=155244.76/min [750000], rate=155172.41/min [760000], rate=154054.05/min [770000], rate=154515.05/min [780000], rate=154966.89/min [790000], rate=155409.84/min [800000], rate=154340.84/min [810000], rate=152830.19/min [820000], rate=152795.03/min [830000], rate=153703.70/min [840000], rate=153658.54/min [850000], rate=154545.45/min [860000], rate=153571.43/min [870000], rate=153529.41/min [880000], rate=153043.48/min [890000], rate=152571.43/min [900000], rate=153846.15/min [910000], rate=154674.22/min [920000], rate=155056.18/min [930000], rate=155000.00/min [940000], rate=154098.36/min [950000], rate=153225.81/min [960000], rate=152380.95/min [970000], rate=150777.20/min [980000], rate=150383.63/min [990000], rate=150761.42/min [1000000], rate=150753.77/min [1010000], rate=151500.00/min [1020000], rate=150738.92/min [1030000], rate=150731.71/min [1040000], rate=150724.64/min [1050000], rate=151442.31/min [1060000], rate=150710.90/min [1070000], rate=150000.00/min [1080000], rate=150000.00/min [1090000], rate=150691.24/min [1100000], rate=150684.93/min [1110000], rate=151020.41/min [1120000], rate=150672.65/min [1130000], rate=151339.29/min [1140000], rate=150660.79/min [1150000], rate=151315.79/min [1160000], rate=151965.07/min [1170000], rate=152941.18/min [1180000], rate=152586.21/min [1190000], rate=137837.84/min [1200000], rate=127433.63/min [1210000], rate=118821.60/min [1220000], rate=111755.73/min [1230000], rate=105882.35/min [1240000], rate=100540.54/min [1250000], rate=95785.44/min [1260000], rate=91194.21/min [1270000], rate=87990.76/min [1280000], rate=84861.88/min [1290000], rate=81991.53/min [1300000], rate=79268.29/min [1310000], rate=77058.82/min [1320000], rate=75000.00/min [1330000], rate=73076.92/min [1340000], rate=71785.71/min [1350000], rate=70496.08/min [1360000], rate=69505.96/min [1370000], rate=68729.10/min [1380000], rate=67980.30/min [1390000], rate=67258.06/min [1400000], rate=66613.80/min [1410000], rate=66093.75/min [1420000], rate=65639.45/min [1430000], rate=65148.06/min [1440000], rate=64622.29/min [1450000], rate=64301.55/min [1460000], rate=63848.40/min [1470000], rate=63316.58/min [1480000], rate=62845.01/min [1490000], rate=62561.23/min [1500000], rate=62500.00/min [1510000], rate=62396.69/min [1520000], rate=62380.30/min [1530000], rate=62195.12/min [1540000], rate=62055.07/min [1550000], rate=62082.78/min [1560000], rate=62151.39/min [1570000], rate=62219.29/min [1580000], rate=62286.47/min [1590000], rate=62434.55/min [1600000], rate=62378.17/min [1610000], rate=62082.26/min [1620000], rate=61871.42/min [1630000], rate=61781.43/min [1640000], rate=61692.79/min [1650000], rate=61682.24/min [1660000], rate=61557.48/min [1670000], rate=61434.70/min [1680000], rate=61239.37/min [1690000], rate=61194.93/min [1700000], rate=61151.08/min [1710000], rate=61107.80/min [1720000], rate=61173.68/min [1730000], rate=61166.76/min [1740000], rate=61267.61/min [1750000], rate=61331.78/min [1760000], rate=61466.82/min [1770000], rate=61600.93/min [1780000], rate=61028.57/min [1790000], rate=60370.99/min [1800000], rate=59471.37/min [1810000], rate=58989.68/min [1820000], rate=58741.26/min [1830000], rate=58560.00/min [1840000], rate=58350.95/min [1850000], rate=58237.15/min [1860000], rate=58094.74/min [1870000], rate=57984.50/min [1880000], rate=57463.07/min [1890000], rate=57157.26/min [1900000], rate=56688.21/min [1910000], rate=56314.50/min [1920000], rate=56167.72/min [1930000], rate=56104.65/min [1940000], rate=55880.94/min [1950000], rate=55661.27/min [1960000], rate=55524.08/min [1970000], rate=55363.00/min [1980000], rate=55204.46/min [1990000], rate=55048.41/min [2000000], rate=54894.78/min [2010000], rate=54743.53/min [2020000], rate=54594.59/min [2030000], rate=54545.45/min [2040000], rate=54496.88/min [2050000], rate=54472.98/min [2060000], rate=54569.54/min [2070000], rate=54665.49/min [2080000], rate=54760.86/min [2090000], rate=54855.64/min [2100000], rate=54973.82/min [2110000], rate=55067.42/min -building interval tree based on /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=20000.00/min [20000], rate=18750.00/min [30000], rate=20689.66/min [40000], rate=22429.91/min [50000], rate=23622.05/min [60000], rate=25714.29/min [70000], rate=26582.28/min [80000], rate=27428.57/min [90000], rate=27551.02/min [100000], rate=28571.43/min [110000], rate=28448.28/min [120000], rate=29149.80/min [130000], rate=30115.83/min [140000], rate=31111.11/min [150000], rate=31914.89/min [160000], rate=32989.69/min [170000], rate=34113.71/min [180000], rate=35409.84/min [190000], rate=36075.95/min [200000], rate=36923.08/min [210000], rate=37951.81/min [220000], rate=39053.25/min [230000], rate=39884.39/min [240000], rate=40449.44/min [250000], rate=40760.87/min [260000], rate=41379.31/min [270000], rate=42187.50/min [280000], rate=42966.75/min [290000], rate=43718.59/min [300000], rate=44776.12/min [310000], rate=45365.85/min [320000], rate=45823.39/min [330000], rate=45517.24/min [340000], rate=45132.74/min [350000], rate=45064.38/min [360000], rate=44813.28/min [370000], rate=44668.01/min [380000], rate=44793.71/min [390000], rate=44827.59/min [400000], rate=45028.14/min [410000], rate=45387.45/min [420000], rate=45818.18/min [430000], rate=46236.56/min [440000], rate=46725.66/min [450000], rate=47120.42/min [460000], rate=47586.21/min [470000], rate=48287.67/min [480000], rate=49146.76/min [490000], rate=49662.16/min [500000], rate=50420.17/min [510000], rate=51256.28/min [520000], rate=51741.29/min [530000], rate=51373.18/min [540000], rate=51023.62/min [550000], rate=50847.46/min [560000], rate=50374.81/min [570000], rate=50368.19/min [580000], rate=51026.39/min [590000], rate=51378.81/min [600000], rate=51428.57/min [610000], rate=51046.03/min [620000], rate=51169.19/min [630000], rate=51428.57/min [640000], rate=51543.62/min [650000], rate=51792.83/min [660000], rate=52173.91/min [670000], rate=52480.42/min [680000], rate=52849.74/min [690000], rate=53213.37/min [700000], rate=52963.43/min [710000], rate=51951.22/min [720000], rate=51124.26/min [730000], rate=50519.03/min [740000], rate=50511.95/min [750000], rate=50962.63/min [760000], rate=51409.24/min [770000], rate=51851.85/min [780000], rate=52290.50/min [790000], rate=52030.74/min [800000], rate=51557.47/min [810000], rate=51211.80/min [820000], rate=51037.34/min [830000], rate=50816.33/min [840000], rate=50551.65/min [850000], rate=50395.26/min [860000], rate=50000.00/min [870000], rate=49619.77/min [880000], rate=49391.96/min [890000], rate=49035.81/min [900000], rate=48957.39/min [910000], rate=48793.57/min [920000], rate=48720.21/min [930000], rate=48691.10/min [940000], rate=48578.81/min [950000], rate=48305.08/min [960000], rate=48403.36/min [970000], rate=48379.05/min [980000], rate=48395.06/min [990000], rate=48097.17/min [1000000], rate=48192.77/min [1010000], rate=48133.44/min [1020000], rate=48075.41/min [1030000], rate=48093.39/min [1040000], rate=47742.92/min [1050000], rate=47727.27/min [1060000], rate=47604.79/min [1070000], rate=47661.47/min [1080000], rate=47647.06/min [1090000], rate=47737.23/min [1100000], rate=47826.09/min [1110000], rate=47982.71/min [1120000], rate=48172.04/min [1130000], rate=48359.49/min [1140000], rate=48614.07/min [1150000], rate=48797.74/min [1160000], rate=48979.59/min [1170000], rate=48514.17/min [1180000], rate=48032.56/min [1190000], rate=47347.48/min [1200000], rate=46875.00/min [1210000], rate=46658.10/min [1220000], rate=46358.45/min [1230000], rate=45981.31/min [1240000], rate=45869.30/min [1250000], rate=45703.84/min [1260000], rate=45597.10/min [1270000], rate=45574.16/min [1280000], rate=45336.48/min [1290000], rate=45183.89/min [1300000], rate=45060.66/min [1310000], rate=44914.29/min [1320000], rate=44796.38/min [1330000], rate=44756.03/min [1340000], rate=44741.24/min [1350000], rate=44603.52/min [1360000], rate=44541.48/min [1370000], rate=44384.45/min [1380000], rate=44325.48/min [1390000], rate=44361.70/min [1400000], rate=44420.94/min [1410000], rate=44549.76/min [1420000], rate=44607.33/min [1430000], rate=44594.59/min [1440000], rate=44697.36/min [1450000], rate=44822.26/min [1460000], rate=44969.20/min [1470000], rate=45068.98/min [1480000], rate=45190.84/min [1490000], rate=45403.76/min [1500000], rate=45662.10/min [1510000], rate=45919.92/min [1520000], rate=46200.61/min [1530000], rate=46481.01/min [1540000], rate=46737.48/min [1550000], rate=46993.43/min [1560000], rate=47153.65/min [1570000], rate=47289.16/min [1580000], rate=47447.45/min [1590000], rate=47557.33/min [1600000], rate=47713.72/min [1610000], rate=47633.14/min [1620000], rate=47230.32/min [1630000], rate=46996.64/min [1640000], rate=46812.56/min [1650000], rate=46544.43/min [1660000], rate=46261.03/min [1670000], rate=46026.64/min [1680000], rate=45735.03/min [1690000], rate=45552.56/min [1700000], rate=45454.55/min [1710000], rate=45620.28/min [1720000], rate=45704.16/min [1730000], rate=45506.36/min [1740000], rate=45371.58/min [1750000], rate=45258.62/min [1760000], rate=45128.21/min [1770000], rate=45038.17/min [1780000], rate=45044.29/min [1790000], rate=45088.16/min [1800000], rate=45131.63/min [1810000], rate=45062.24/min [1820000], rate=45086.71/min [1830000], rate=45166.60/min [1840000], rate=45245.90/min [1850000], rate=45306.12/min [1860000], rate=45365.85/min [1870000], rate=45443.50/min [1880000], rate=45502.22/min [1890000], rate=45615.45/min [1900000], rate=45709.70/min [1910000], rate=45821.67/min [1920000], rate=45933.01/min [1930000], rate=46043.74/min [1940000], rate=46153.85/min [1950000], rate=46299.96/min [1960000], rate=46427.16/min [1970000], rate=46572.10/min [1980000], rate=46716.48/min [1990000], rate=46878.68/min [2000000], rate=46875.00/min [2010000], rate=46816.77/min [2020000], rate=46759.26/min [2030000], rate=46756.24/min [2040000], rate=46753.25/min [2050000], rate=46750.29/min [2060000], rate=46729.68/min [2070000], rate=46726.86/min [2080000], rate=46759.09/min [2090000], rate=46791.04/min [2100000], rate=46822.74/min [2110000], rate=46906.26/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir --filt_file /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.nhLzySAF68/./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... 8000000.00 reads per min processed... 10000000.00 reads per min processed... 9000000.00 reads per min processed... 10500000.00 reads per min processed... 9600000.00 reads per min processed... 10800000.00 reads per min processed... 10000000.00 reads per min processed... 9428571.43 reads per min processed... 9000000.00 reads per min processed... 7800000.00 reads per min processed... 7636363.64 reads per min processed... 7500000.00 reads per min processed... 7384615.38 reads per min processed... 6800000.00 reads per min processed... 6750000.00 reads per min processed... 6705882.35 reads per min processed... 6315789.47 reads per min processed... 6300000.00 reads per min processed... 6285714.29 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 5769230.77 reads per min processed... 5777777.78 reads per min processed... 5586206.90 reads per min processed... 5419354.84 reads per min processed... 5437500.00 reads per min processed... 5454545.45 reads per min processed... 5314285.71 reads per min processed... 5333333.33 reads per min processed... 5351351.35 reads per min processed... 5368421.05 reads per min processed... 5384615.38 reads per min processed... 5268292.68 reads per min processed... 5285714.29 reads per min processed... 5302325.58 reads per min processed... 5318181.82 reads per min processed... 5333333.33 reads per min processed... 5347826.09 reads per min processed... 5361702.13 reads per min processed... 5489361.70 reads per min processed... 5500000.00 reads per min processed... 5625000.00 reads per min processed... 5632653.06 reads per min processed... 5640000.00 reads per min processed... 5760000.00 reads per min processed... 5764705.88 reads per min processed... 5882352.94 reads per min processed... 5773584.91 reads per min processed... 5777777.78 reads per min processed... 5781818.18 reads per min processed... 5785714.29 reads per min processed... 5689655.17 reads per min processed... 5694915.25 reads per min processed... 5700000.00 reads per min processed... 5704918.03 reads per min processed... 5709677.42 reads per min processed... 5714285.71 reads per min processed... 5630769.23 reads per min processed... 5636363.64 reads per min processed... 5558823.53 reads per min processed... 5485714.29 reads per min processed... 5492957.75 reads per min processed... 5424657.53 reads per min processed... 5360000.00 reads per min processed... 5368421.05 reads per min processed... 5376623.38 reads per min processed... 5316455.70 reads per min processed... 5325000.00 reads per min processed... 5333333.33 reads per min processed... 5341463.41 reads per min processed... 5349397.59 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.nhLzySAF68/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.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.nhLzySAF68/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -112494.361475 EM: Round [1] log likelihood: -112175.484426 EM: Round [2] log likelihood: -112048.788578 EM: Round [3] log likelihood: -111986.608629 EM: Round [4] log likelihood: -111952.783192 EM: Round [5] log likelihood: -111933.322613 EM: Round [6] log likelihood: -111921.648124 EM: Round [7] log likelihood: -111914.353125 EM: Round [8] log likelihood: -111909.603440 EM: Round [9] log likelihood: -111906.387806 EM: Round [10] log likelihood: -111904.133204 EM: Round [11] log likelihood: -111902.503905 EM: Round [12] log likelihood: -111901.295896 EM: Round [13] log likelihood: -111900.380619 EM: Round [14] log likelihood: -111899.674254 EM: Round [15] log likelihood: -111899.120440 EM: Round [16] log likelihood: -111898.680238 EM: Round [17] log likelihood: -111898.326100 EM: Round [18] log likelihood: -111898.038132 EM: Round [19] log likelihood: -111897.801711 EM: Round [20] log likelihood: -111897.605917 EM: Round [21] log likelihood: -111897.442481 EM: Round [22] log likelihood: -111897.305065 EM: Round [23] log likelihood: -111897.188755 EM: Round [24] log likelihood: -111897.089704 EM: Round [25] log likelihood: -111897.004870 EM: Round [26] log likelihood: -111896.931828 EM: Round [27] log likelihood: -111896.868628 EM: Round [28] log likelihood: -111896.813691 EM: Round [29] log likelihood: -111896.765731 EM: Round [30] log likelihood: -111896.723690 EM: Round [31] log likelihood: -111896.686697 EM: Round [32] log likelihood: -111896.654028 EM: Round [33] log likelihood: -111896.625078 EM: Round [34] log likelihood: -111896.599339 EM: Round [35] log likelihood: -111896.576385 EM: Round [36] log likelihood: -111896.555853 EM: Round [37] log likelihood: -111896.537435 EM: Round [38] log likelihood: -111896.520869 EM: Round [39] log likelihood: -111896.505929 EM: Round [40] log likelihood: -111896.492423 EM: Round [41] log likelihood: -111896.480182 EM: Round [42] log likelihood: -111896.469062 EM: Round [43] log likelihood: -111896.458939 EM: Round [44] log likelihood: -111896.449702 EM: Round [45] log likelihood: -111896.441256 EM: Round [46] log likelihood: -111896.433518 EM: Round [47] log likelihood: -111896.426413 EM: Round [48] log likelihood: -111896.419879 EM: Round [49] log likelihood: -111896.413858 EM: Round [50] log likelihood: -111896.408299 EM: Round [51] log likelihood: -111896.403158 EM: Round [52] log likelihood: -111896.398396 EM: Round [53] log likelihood: -111896.393977 EM: Round [54] log likelihood: -111896.389871 EM: Round [55] log likelihood: -111896.386048 EM: Round [56] log likelihood: -111896.382485 EM: Round [57] log likelihood: -111896.379159 EM: Round [58] log likelihood: -111896.376049 EM: Round [59] log likelihood: -111896.373138 EM: Round [60] log likelihood: -111896.370409 EM: Round [61] log likelihood: -111896.367847 EM: Round [62] log likelihood: -111896.365440 EM: Round [63] log likelihood: -111896.363176 EM: Round [64] log likelihood: -111896.361043 EM: Round [65] log likelihood: -111896.359031 EM: Round [66] log likelihood: -111896.357132 EM: Round [67] log likelihood: -111896.355338 EM: Round [68] log likelihood: -111896.353640 EM: Round [69] log likelihood: -111896.352033 EM: Round [70] log likelihood: -111896.350510 EM: Round [71] log likelihood: -111896.349065 EM: Round [72] log likelihood: -111896.347693 EM: Round [73] log likelihood: -111896.346390 EM: Round [74] log likelihood: -111896.345151 EM: Round [75] log likelihood: -111896.343971 EM: Round [76] log likelihood: -111896.342847 EM: Round [77] log likelihood: -111896.341777 EM: Round [78] log likelihood: -111896.340755 EM: Round [79] log likelihood: -111896.339781 EM: Round [80] log likelihood: -111896.338850 EM: Round [81] log likelihood: -111896.337961 EM: Round [82] log likelihood: -111896.337110 EM: Round [83] log likelihood: -111896.336297 EM: Round [84] log likelihood: -111896.335518 EM: Round [85] log likelihood: -111896.334772 EM: Round [86] log likelihood: -111896.334057 EM: Round [87] log likelihood: -111896.333372 EM: Round [88] log likelihood: -111896.332715 EM: Round [89] log likelihood: -111896.332084 EM: Round [90] log likelihood: -111896.331479 EM: Round [91] log likelihood: -111896.330897 EM: Round [92] log likelihood: -111896.330338 EM: Round [93] log likelihood: -111896.329801 EM: Round [94] log likelihood: -111896.329285 EM: Round [95] log likelihood: -111896.328788 EM: Round [96] log likelihood: -111896.328310 EM: Round [97] log likelihood: -111896.327849 EM: Round [98] log likelihood: -111896.327406 EM: Round [99] log likelihood: -111896.326979 EM: Round [100] log likelihood: -111896.326568 EM: Round [101] log likelihood: -111896.326171 EM: Round [102] log likelihood: -111896.325788 EM: Round [103] log likelihood: -111896.325420 EM: Round [104] log likelihood: -111896.325064 EM: Round [105] log likelihood: -111896.324720 EM: Round [106] log likelihood: -111896.324389 EM: Round [107] log likelihood: -111896.324068 EM: Round [108] log likelihood: -111896.323759 EM: Round [109] log likelihood: -111896.323460 EM: Round [110] log likelihood: -111896.323172 EM: Round [111] log likelihood: -111896.322892 EM: Round [112] log likelihood: -111896.322623 EM: Round [113] log likelihood: -111896.322362 EM: Round [114] log likelihood: -111896.322109 EM: Round [115] log likelihood: -111896.321865 EM: Round [116] log likelihood: -111896.321629 EM: Round [117] log likelihood: -111896.321400 EM: Round [118] log likelihood: -111896.321179 EM: Round [119] log likelihood: -111896.320965 EM: Round [120] log likelihood: -111896.320757 EM: Round [121] log likelihood: -111896.320556 EM: Round [122] log likelihood: -111896.320361 EM: Round [123] log likelihood: -111896.320172 EM: Round [124] log likelihood: -111896.319989 EM: Round [125] log likelihood: -111896.319812 EM: Round [126] log likelihood: -111896.319640 EM: Round [127] log likelihood: -111896.319473 EM: Round [128] log likelihood: -111896.319311 EM: Round [129] log likelihood: -111896.319154 EM: Round [130] log likelihood: -111896.319002 EM: Round [131] log likelihood: -111896.318854 EM: Round [132] log likelihood: -111896.318711 EM: Round [133] log likelihood: -111896.318571 EM: Round [134] log likelihood: -111896.318436 EM: Round [135] log likelihood: -111896.318305 EM: Round [136] log likelihood: -111896.318177 EM: Round [137] log likelihood: -111896.318054 EM: Round [138] log likelihood: -111896.317933 EM: Round [139] log likelihood: -111896.317816 EM: Round [140] log likelihood: -111896.317703 EM: Round [141] log likelihood: -111896.317592 EM: Round [142] log likelihood: -111896.317485 EM: Round [143] log likelihood: -111896.317380 EM: Round [144] log likelihood: -111896.317279 EM: Round [145] log likelihood: -111896.317180 EM: Stopping iterations at round 145 due to insufficient improvement in likelihood. EM: Starting log likelihood: -112365.910957 EM: Round [1] log likelihood: -112092.139743 EM: Round [2] log likelihood: -111990.174493 EM: Round [3] log likelihood: -111942.121346 EM: Round [4] log likelihood: -111916.625851 EM: Round [5] log likelihood: -111902.200300 EM: Round [6] log likelihood: -111893.651299 EM: Round [7] log likelihood: -111888.359932 EM: Round [8] log likelihood: -111884.940377 EM: Round [9] log likelihood: -111882.638071 EM: Round [10] log likelihood: -111881.029924 EM: Round [11] log likelihood: -111879.870415 EM: Round [12] log likelihood: -111879.011648 EM: Round [13] log likelihood: -111878.361127 EM: Round [14] log likelihood: -111877.858917 EM: Round [15] log likelihood: -111877.464902 EM: Round [16] log likelihood: -111877.151453 EM: Round [17] log likelihood: -111876.899064 EM: Round [18] log likelihood: -111876.693657 EM: Round [19] log likelihood: -111876.524887 EM: Round [20] log likelihood: -111876.385022 EM: Round [21] log likelihood: -111876.268205 EM: Round [22] log likelihood: -111876.169938 EM: Round [23] log likelihood: -111876.086732 EM: Round [24] log likelihood: -111876.015850 EM: Round [25] log likelihood: -111875.955126 EM: Round [26] log likelihood: -111875.902830 EM: Round [27] log likelihood: -111875.857570 EM: Round [28] log likelihood: -111875.818218 EM: Round [29] log likelihood: -111875.783855 EM: Round [30] log likelihood: -111875.753724 EM: Round [31] log likelihood: -111875.727201 EM: Round [32] log likelihood: -111875.703767 EM: Round [33] log likelihood: -111875.682989 EM: Round [34] log likelihood: -111875.664504 EM: Round [35] log likelihood: -111875.648006 EM: Round [36] log likelihood: -111875.633235 EM: Round [37] log likelihood: -111875.619972 EM: Round [38] log likelihood: -111875.608028 EM: Round [39] log likelihood: -111875.597243 EM: Round [40] log likelihood: -111875.587478 EM: Round [41] log likelihood: -111875.578613 EM: Round [42] log likelihood: -111875.570547 EM: Round [43] log likelihood: -111875.563188 EM: Round [44] log likelihood: -111875.556460 EM: Round [45] log likelihood: -111875.550295 EM: Round [46] log likelihood: -111875.544632 EM: Round [47] log likelihood: -111875.539420 EM: Round [48] log likelihood: -111875.534613 EM: Round [49] log likelihood: -111875.530171 EM: Round [50] log likelihood: -111875.526058 EM: Round [51] log likelihood: -111875.522243 EM: Round [52] log likelihood: -111875.518697 EM: Round [53] log likelihood: -111875.515395 EM: Round [54] log likelihood: -111875.512317 EM: Round [55] log likelihood: -111875.509441 EM: Round [56] log likelihood: -111875.506750 EM: Round [57] log likelihood: -111875.504229 EM: Round [58] log likelihood: -111875.501862 EM: Round [59] log likelihood: -111875.499639 EM: Round [60] log likelihood: -111875.497546 EM: Round [61] log likelihood: -111875.495574 EM: Round [62] log likelihood: -111875.493713 EM: Round [63] log likelihood: -111875.491956 EM: Round [64] log likelihood: -111875.490293 EM: Round [65] log likelihood: -111875.488719 EM: Round [66] log likelihood: -111875.487227 EM: Round [67] log likelihood: -111875.485811 EM: Round [68] log likelihood: -111875.484466 EM: Round [69] log likelihood: -111875.483188 EM: Round [70] log likelihood: -111875.481971 EM: Round [71] log likelihood: -111875.480812 EM: Round [72] log likelihood: -111875.479707 EM: Round [73] log likelihood: -111875.478653 EM: Round [74] log likelihood: -111875.477647 EM: Round [75] log likelihood: -111875.476686 EM: Round [76] log likelihood: -111875.475767 EM: Round [77] log likelihood: -111875.474888 EM: Round [78] log likelihood: -111875.474046 EM: Round [79] log likelihood: -111875.473240 EM: Round [80] log likelihood: -111875.472467 EM: Round [81] log likelihood: -111875.471726 EM: Round [82] log likelihood: -111875.471014 EM: Round [83] log likelihood: -111875.470332 EM: Round [84] log likelihood: -111875.469676 EM: Round [85] log likelihood: -111875.469046 EM: Round [86] log likelihood: -111875.468440 EM: Round [87] log likelihood: -111875.467857 EM: Round [88] log likelihood: -111875.467297 EM: Round [89] log likelihood: -111875.466757 EM: Round [90] log likelihood: -111875.466238 EM: Round [91] log likelihood: -111875.465737 EM: Round [92] log likelihood: -111875.465255 EM: Round [93] log likelihood: -111875.464790 EM: Round [94] log likelihood: -111875.464342 EM: Round [95] log likelihood: -111875.463910 EM: Round [96] log likelihood: -111875.463493 EM: Round [97] log likelihood: -111875.463090 EM: Round [98] log likelihood: -111875.462702 EM: Round [99] log likelihood: -111875.462327 EM: Round [100] log likelihood: -111875.461964 EM: Round [101] log likelihood: -111875.461614 EM: Round [102] log likelihood: -111875.461276 EM: Round [103] log likelihood: -111875.460949 EM: Round [104] log likelihood: -111875.460633 EM: Round [105] log likelihood: -111875.460328 EM: Round [106] log likelihood: -111875.460032 EM: Round [107] log likelihood: -111875.459746 EM: Round [108] log likelihood: -111875.459469 EM: Round [109] log likelihood: -111875.459202 EM: Round [110] log likelihood: -111875.458943 EM: Round [111] log likelihood: -111875.458692 EM: Round [112] log likelihood: -111875.458449 EM: Round [113] log likelihood: -111875.458214 EM: Round [114] log likelihood: -111875.457986 EM: Round [115] log likelihood: -111875.457765 EM: Round [116] log likelihood: -111875.457551 EM: Round [117] log likelihood: -111875.457344 EM: Round [118] log likelihood: -111875.457143 EM: Round [119] log likelihood: -111875.456948 EM: Round [120] log likelihood: -111875.456759 EM: Round [121] log likelihood: -111875.456576 EM: Round [122] log likelihood: -111875.456398 EM: Round [123] log likelihood: -111875.456226 EM: Round [124] log likelihood: -111875.456059 EM: Round [125] log likelihood: -111875.455896 EM: Round [126] log likelihood: -111875.455739 EM: Round [127] log likelihood: -111875.455586 EM: Round [128] log likelihood: -111875.455438 EM: Round [129] log likelihood: -111875.455294 EM: Round [130] log likelihood: -111875.455154 EM: Round [131] log likelihood: -111875.455018 EM: Round [132] log likelihood: -111875.454886 EM: Round [133] log likelihood: -111875.454758 EM: Round [134] log likelihood: -111875.454633 EM: Round [135] log likelihood: -111875.454513 EM: Round [136] log likelihood: -111875.454395 EM: Round [137] log likelihood: -111875.454281 EM: Round [138] log likelihood: -111875.454170 EM: Round [139] log likelihood: -111875.454062 EM: Round [140] log likelihood: -111875.453957 EM: Round [141] log likelihood: -111875.453855 EM: Round [142] log likelihood: -111875.453756 EM: Stopping iterations at round 142 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 106860155 > /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir > /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir --annotate /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir -done, see /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 467, filtered: 5219) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/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 [ENSG00000276168.1] WARNING, no entry stored in dbm for [ENSG00000240116.3] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000270195.2] WARNING, no entry stored in dbm for [ENSG00000270195.2] WARNING, no entry stored in dbm for [ENSG00000275716.1] WARNING, no entry stored in dbm for [ENSG00000263883.1] WARNING, no entry stored in dbm for [ENSG00000203262.3] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000220685.3] WARNING, no entry stored in dbm for [ENSG00000280248.1] 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 [ENSG00000266677.1] WARNING, no entry stored in dbm for [ENSG00000205682.2] WARNING, no entry stored in dbm for [ENSG00000261963.3] WARNING, no entry stored in dbm for [ENSG00000167798.17] WARNING, no entry stored in dbm for [ENSG00000288554.1] WARNING, no entry stored in dbm for [ENSG00000286864.1] WARNING, no entry stored in dbm for [ENSG00000279437.1] WARNING, no entry stored in dbm for [ENSG00000185596.16] 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 [ENSG00000249180.1] WARNING, no entry stored in dbm for [ENSG00000227195.11] WARNING, no entry stored in dbm for [ENSG00000180438.15] WARNING, no entry stored in dbm for [ENSG00000253798.2] WARNING, no entry stored in dbm for [ENSG00000233511.1] 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 [ENSG00000229436.1] WARNING, no entry stored in dbm for [ENSG00000287419.1] WARNING, no entry stored in dbm for [ENSG00000224425.2] WARNING, no entry stored in dbm for [ENSG00000237307.2] WARNING, no entry stored in dbm for [ENSG00000232732.11] WARNING, no entry stored in dbm for [ENSG00000196295.12] WARNING, no entry stored in dbm for [ENSG00000247925.2] WARNING, no entry stored in dbm for [ENSG00000241743.4] WARNING, no entry stored in dbm for [ENSG00000262662.1] WARNING, no entry stored in dbm for [ENSG00000213642.3] WARNING, no entry stored in dbm for [ENSG00000244215.2] WARNING, no entry stored in dbm for [ENSG00000225678.2] WARNING, no entry stored in dbm for [ENSG00000229140.11] WARNING, no entry stored in dbm for [ENSG00000218565.2] WARNING, no entry stored in dbm for [ENSG00000215030.5] WARNING, no entry stored in dbm for [ENSG00000215030.5] WARNING, no entry stored in dbm for [ENSG00000274585.1] WARNING, no entry stored in dbm for [ENSG00000205763.13] WARNING, no entry stored in dbm for [ENSG00000264275.1] WARNING, no entry stored in dbm for [ENSG00000243738.3] WARNING, no entry stored in dbm for [ENSG00000201428.1] WARNING, no entry stored in dbm for [ENSG00000200047.1] WARNING, no entry stored in dbm for [ENSG00000222210.1] WARNING, no entry stored in dbm for [ENSG00000222068.1] WARNING, no entry stored in dbm for [ENSG00000200488.1] WARNING, no entry stored in dbm for [ENSG00000200047.1] WARNING, no entry stored in dbm for [ENSG00000222774.1] WARNING, no entry stored in dbm for [ENSG00000222068.1] WARNING, no entry stored in dbm for [ENSG00000282851.2] WARNING, no entry stored in dbm for [ENSG00000261087.1] WARNING, no entry stored in dbm for [ENSG00000245532.9] WARNING, no entry stored in dbm for [ENSG00000250198.3] WARNING, no entry stored in dbm for [ENSG00000277654.6] WARNING, no entry stored in dbm for [ENSG00000286558.1] WARNING, no entry stored in dbm for [ENSG00000180279.7] WARNING, no entry stored in dbm for [ENSG00000215448.3] WARNING, no entry stored in dbm for [ENSG00000233325.3] WARNING, no entry stored in dbm for [ENSG00000228998.4] WARNING, no entry stored in dbm for [ENSG00000286447.1] WARNING, no entry stored in dbm for [ENSG00000235267.1] WARNING, no entry stored in dbm for [ENSG00000255875.2] WARNING, no entry stored in dbm for [ENSG00000255875.2] WARNING, no entry stored in dbm for [ENSG00000261963.3] WARNING, no entry stored in dbm for [ENSG00000259573.1] WARNING, no entry stored in dbm for [ENSG00000286087.1] WARNING, no entry stored in dbm for [ENSG00000286087.1] WARNING, no entry stored in dbm for [ENSG00000254453.1] WARNING, no entry stored in dbm for [ENSG00000277047.5] WARNING, no entry stored in dbm for [ENSG00000176728.10] WARNING, no entry stored in dbm for [ENSG00000253230.9] WARNING, no entry stored in dbm for [ENSG00000267391.5] WARNING, no entry stored in dbm for [ENSG00000174403.16] WARNING, no entry stored in dbm for [ENSG00000231367.6] WARNING, no entry stored in dbm for [ENSG00000241621.1] WARNING, no entry stored in dbm for [ENSG00000187172.15] WARNING, no entry stored in dbm for [ENSG00000233492.2] WARNING, no entry stored in dbm for [ENSG00000227082.3] WARNING, no entry stored in dbm for [ENSG00000258998.2] WARNING, no entry stored in dbm for [ENSG00000258998.2] WARNING, no entry stored in dbm for [ENSG00000267779.7] WARNING, no entry stored in dbm for [ENSG00000251219.2] WARNING, no entry stored in dbm for [ENSG00000205396.11] WARNING, no entry stored in dbm for [ENSG00000170858.10] WARNING, no entry stored in dbm for [ENSG00000170858.10] WARNING, no entry stored in dbm for [ENSG00000213016.3] WARNING, no entry stored in dbm for [ENSG00000260807.7] WARNING, no entry stored in dbm for [ENSG00000279080.1] WARNING, no entry stored in dbm for [ENSG00000279738.1] WARNING, no entry stored in dbm for [ENSG00000240668.1] WARNING, no entry stored in dbm for [ENSG00000204959.4] WARNING, no entry stored in dbm for [ENSG00000224924.7] WARNING, no entry stored in dbm for [ENSG00000240731.1] WARNING, no entry stored in dbm for [ENSG00000249286.1] WARNING, no entry stored in dbm for [ENSG00000215498.9] WARNING, no entry stored in dbm for [ENSG00000230590.11] WARNING, no entry stored in dbm for [ENSG00000259722.2] WARNING, no entry stored in dbm for [ENSG00000225851.1] WARNING, no entry stored in dbm for [ENSG00000203650.9] WARNING, no entry stored in dbm for [ENSG00000228564.2] WARNING, no entry stored in dbm for [ENSG00000232628.6] WARNING, no entry stored in dbm for [ENSG00000281344.1] WARNING, no entry stored in dbm for [ENSG00000166104.15] WARNING, no entry stored in dbm for [ENSG00000214433.4] WARNING, no entry stored in dbm for [ENSG00000249906.1] WARNING, no entry stored in dbm for [ENSG00000216360.1] WARNING, no entry stored in dbm for [ENSG00000215483.11] WARNING, no entry stored in dbm for [ENSG00000215483.11] WARNING, no entry stored in dbm for [ENSG00000283907.1] WARNING, no entry stored in dbm for [ENSG00000242613.1] WARNING, no entry stored in dbm for [ENSG00000232044.7] WARNING, no entry stored in dbm for [ENSG00000271848.2] WARNING, no entry stored in dbm for [ENSG00000223912.1] WARNING, no entry stored in dbm for [ENSG00000231162.4] WARNING, no entry stored in dbm for [ENSG00000186704.9] WARNING, no entry stored in dbm for [ENSG00000242435.1] WARNING, no entry stored in dbm for [ENSG00000249628.3] WARNING, no entry stored in dbm for [ENSG00000209482.1] WARNING, no entry stored in dbm for [ENSG00000283541.1] WARNING, no entry stored in dbm for [ENSG00000225005.1] WARNING, no entry stored in dbm for [ENSG00000272157.1] WARNING, no entry stored in dbm for [ENSG00000285367.1] WARNING, no entry stored in dbm for [ENSG00000241104.5] WARNING, no entry stored in dbm for [ENSG00000260902.1] WARNING, no entry stored in dbm for [ENSG00000230558.2] WARNING, no entry stored in dbm for [ENSG00000223705.9] WARNING, no entry stored in dbm for [ENSG00000203993.6] WARNING, no entry stored in dbm for [ENSG00000257894.2] WARNING, no entry stored in dbm for [ENSG00000203799.13] WARNING, no entry stored in dbm for [ENSG00000236901.6] WARNING, no entry stored in dbm for [ENSG00000251957.1] WARNING, no entry stored in dbm for [ENSG00000279021.1] WARNING, no entry stored in dbm for [ENSG00000257252.6] WARNING, no entry stored in dbm for [ENSG00000213046.4] WARNING, no entry stored in dbm for [ENSG00000256108.1] WARNING, no entry stored in dbm for [ENSG00000266441.1] WARNING, no entry stored in dbm for [ENSG00000182021.10] WARNING, no entry stored in dbm for [ENSG00000235749.3] WARNING, no entry stored in dbm for [ENSG00000235605.1] WARNING, no entry stored in dbm for [ENSG00000266680.1] WARNING, no entry stored in dbm for [ENSG00000197558.13] WARNING, no entry stored in dbm for [ENSG00000216519.2] WARNING, no entry stored in dbm for [ENSG00000279738.1] WARNING, no entry stored in dbm for [ENSG00000215353.2] WARNING, no entry stored in dbm for [ENSG00000278983.1] WARNING, no entry stored in dbm for [ENSG00000236263.1] WARNING, no entry stored in dbm for [ENSG00000283662.1] WARNING, no entry stored in dbm for [ENSG00000285668.1] WARNING, no entry stored in dbm for [ENSG00000235421.1] WARNING, no entry stored in dbm for [ENSG00000227113.2] WARNING, no entry stored in dbm for [ENSG00000271943.2] WARNING, no entry stored in dbm for [ENSG00000237666.2] WARNING, no entry stored in dbm for [ENSG00000243503.2] WARNING, no entry stored in dbm for [ENSG00000280362.1] WARNING, no entry stored in dbm for [ENSG00000261586.2] WARNING, no entry stored in dbm for [ENSG00000254581.1] WARNING, no entry stored in dbm for [ENSG00000235027.1] WARNING, no entry stored in dbm for [ENSG00000234017.1] WARNING, no entry stored in dbm for [ENSG00000272267.2] WARNING, no entry stored in dbm for [ENSG00000205682.2] WARNING, no entry stored in dbm for [ENSG00000205682.2] WARNING, no entry stored in dbm for [ENSG00000205682.2] WARNING, no entry stored in dbm for [ENSG00000286970.1] WARNING, no entry stored in dbm for [ENSG00000218175.2] WARNING, no entry stored in dbm for [ENSG00000188850.9] WARNING, no entry stored in dbm for [ENSG00000093100.13] 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 [ENSG00000268460.2] WARNING, no entry stored in dbm for [ENSG00000278920.1] WARNING, no entry stored in dbm for [ENSG00000239224.3] WARNING, no entry stored in dbm for [ENSG00000241057.2] WARNING, no entry stored in dbm for [ENSG00000228204.2] WARNING, no entry stored in dbm for [ENSG00000228113.7] * STAR-Fusion complete. See output: /tmp/nxf.nhLzySAF68/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)