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/28/f41d78578200ea95b538a8983dc8e3/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/9b3981fd9fede9c08b406c4f731244/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/41f54a20152b67ec087fd421f9e34a/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/9b3981fd9fede9c08b406c4f731244/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/f41d78578200ea95b538a8983dc8e3/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.lT9KTs8yqN/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary -sample contains 211551416 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir -J /tmp/nxf.lT9KTs8yqN/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.lT9KTs8yqN/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=20000.00/min [20000], rate=19354.84/min [30000], rate=20689.66/min [40000], rate=20338.98/min [50000], rate=20134.23/min [60000], rate=20224.72/min [70000], rate=21105.53/min [80000], rate=22325.58/min [90000], rate=22500.00/min [100000], rate=23076.92/min [110000], rate=23487.54/min [120000], rate=23841.06/min [130000], rate=24148.61/min [140000], rate=23863.64/min [150000], rate=23684.21/min [160000], rate=24000.00/min [170000], rate=24519.23/min [180000], rate=25000.00/min [190000], rate=25560.54/min [200000], rate=26143.79/min [210000], rate=26526.32/min [220000], rate=26720.65/min [230000], rate=27058.82/min [240000], rate=27376.43/min [250000], rate=27726.43/min [260000], rate=27758.01/min [270000], rate=28173.91/min [280000], rate=28093.65/min [290000], rate=28292.68/min [300000], rate=28616.85/min [310000], rate=28837.21/min [320000], rate=29268.29/min [330000], rate=29508.20/min [340000], rate=29737.61/min [350000], rate=29619.18/min [360000], rate=28685.26/min [370000], rate=28244.27/min [380000], rate=27804.88/min [390000], rate=27368.42/min [400000], rate=26637.07/min [410000], rate=25922.02/min [420000], rate=25275.83/min [430000], rate=25097.28/min [440000], rate=24742.27/min [450000], rate=24657.53/min [460000], rate=24577.03/min [470000], rate=24479.17/min [480000], rate=24386.11/min [490000], rate=24137.93/min [500000], rate=24193.55/min [510000], rate=24094.49/min [520000], rate=24000.00/min [530000], rate=23749.07/min [540000], rate=23858.62/min [550000], rate=23895.73/min [560000], rate=23914.59/min [570000], rate=23882.68/min [580000], rate=24049.76/min [590000], rate=24246.58/min [600000], rate=24406.78/min [610000], rate=24514.40/min [620000], rate=24570.67/min [630000], rate=24705.88/min [640000], rate=24806.20/min [650000], rate=24920.13/min [660000], rate=25079.16/min [670000], rate=25203.76/min [680000], rate=25294.48/min [690000], rate=25383.20/min [700000], rate=25531.91/min [710000], rate=25647.20/min [720000], rate=25791.04/min [730000], rate=25917.16/min [740000], rate=26041.06/min [750000], rate=26117.24/min [760000], rate=26267.28/min [770000], rate=26384.92/min [780000], rate=26545.66/min [790000], rate=26704.23/min [800000], rate=26800.67/min [810000], rate=26955.07/min [820000], rate=27107.44/min [830000], rate=27183.41/min [840000], rate=27361.56/min [850000], rate=27552.67/min [860000], rate=27771.80/min [870000], rate=27944.33/min [880000], rate=28160.00/min [890000], rate=28464.82/min [900000], rate=28738.69/min [910000], rate=29011.69/min [920000], rate=29190.90/min [930000], rate=29368.42/min [940000], rate=29559.75/min [950000], rate=29641.19/min [960000], rate=29829.10/min [970000], rate=30015.47/min [980000], rate=30122.95/min [990000], rate=30275.23/min [1000000], rate=30456.85/min [1010000], rate=30652.50/min [1020000], rate=30846.77/min [1030000], rate=31055.28/min [1040000], rate=31215.61/min [1050000], rate=31219.03/min [1060000], rate=31207.07/min [1070000], rate=31225.68/min [1080000], rate=31304.35/min [1090000], rate=31336.85/min [1100000], rate=31428.57/min [1110000], rate=31563.98/min [1120000], rate=31683.17/min [1130000], rate=31786.22/min [1140000], rate=31858.41/min [1150000], rate=31914.89/min [1160000], rate=32000.00/min [1170000], rate=32113.45/min [1180000], rate=32225.76/min [1190000], rate=32293.08/min [1200000], rate=32345.01/min [1210000], rate=32468.69/min [1220000], rate=32518.88/min [1230000], rate=32654.87/min [1240000], rate=32804.23/min [1250000], rate=32952.55/min [1260000], rate=33056.41/min [1270000], rate=33188.15/min [1280000], rate=33347.81/min [1290000], rate=33419.69/min [1300000], rate=33476.39/min [1310000], rate=33632.86/min [1320000], rate=33875.11/min [1330000], rate=34117.14/min [1340000], rate=34329.63/min [1350000], rate=34571.06/min [1360000], rate=34812.29/min [1370000], rate=35053.30/min [1380000], rate=35279.08/min [1390000], rate=35519.59/min [1400000], rate=35759.90/min [1410000], rate=35969.39/min [1420000], rate=36224.49/min [1430000], rate=36464.09/min [1440000], rate=36703.48/min [1450000], rate=36942.68/min [1460000], rate=37118.64/min [1470000], rate=37357.05/min [1480000], rate=37595.26/min [1490000], rate=37833.26/min [1500000], rate=38071.07/min [1510000], rate=38243.98/min [1520000], rate=38383.84/min [1530000], rate=38361.89/min [1540000], rate=38500.00/min [1550000], rate=38541.23/min [1560000], rate=38661.71/min [1570000], rate=38829.35/min [1580000], rate=38964.24/min [1590000], rate=39066.34/min [1600000], rate=39087.95/min [1610000], rate=39268.29/min [1620000], rate=39480.10/min [1630000], rate=39691.56/min [1640000], rate=39918.86/min [1650000], rate=40145.99/min [1660000], rate=40372.92/min [1670000], rate=40583.23/min [1680000], rate=40661.56/min [1690000], rate=40722.89/min [1700000], rate=40734.82/min [1710000], rate=40762.81/min [1720000], rate=40710.06/min [1730000], rate=40610.33/min [1740000], rate=40765.33/min [1750000], rate=40951.64/min [1760000], rate=41169.59/min [1770000], rate=41371.25/min [1780000], rate=41588.79/min [1790000], rate=41806.15/min [1800000], rate=42023.35/min [1810000], rate=42240.37/min [1820000], rate=42457.23/min [1830000], rate=42657.34/min [1840000], rate=42873.79/min [1850000], rate=42973.29/min [1860000], rate=43122.10/min [1870000], rate=43353.94/min [1880000], rate=43568.95/min [1890000], rate=43783.78/min [1900000], rate=43863.02/min [1910000], rate=43908.05/min [1920000], rate=44036.70/min [1930000], rate=44131.10/min [1940000], rate=44174.57/min [1950000], rate=44234.40/min [1960000], rate=44227.15/min [1970000], rate=44386.03/min [1980000], rate=44594.59/min [1990000], rate=44769.40/min [2000000], rate=44977.51/min [2010000], rate=45185.46/min [2020000], rate=45393.26/min [2030000], rate=45600.90/min [2040000], rate=45791.25/min [2050000], rate=45998.50/min [2060000], rate=46205.61/min [2070000], rate=46360.58/min [2080000], rate=46584.55/min [2090000], rate=46791.04/min [2100000], rate=46997.39/min [2110000], rate=47185.99/min [2120000], rate=47339.04/min [2130000], rate=47562.34/min [2140000], rate=47767.86/min [2150000], rate=47973.22/min [2160000], rate=48160.54/min [2170000], rate=48257.97/min [2180000], rate=48301.33/min [2190000], rate=48415.62/min [2200000], rate=48493.75/min [2210000], rate=48553.64/min [2220000], rate=48666.42/min [2230000], rate=48778.71/min [2240000], rate=48890.51/min [2250000], rate=48948.51/min [2260000], rate=49041.59/min [2270000], rate=49205.20/min [2280000], rate=49368.46/min [2290000], rate=49549.22/min [2300000], rate=49729.73/min [2310000], rate=49927.95/min [2320000], rate=50126.04/min [2330000], rate=50305.87/min [2340000], rate=50503.60/min [2350000], rate=50682.96/min [2360000], rate=50898.63/min [2370000], rate=51095.94/min [2380000], rate=51293.10/min [2390000], rate=51471.64/min [2400000], rate=51668.46/min [2410000], rate=51865.14/min [2420000], rate=52061.67/min [2430000], rate=52258.06/min [2440000], rate=52454.32/min [2450000], rate=52650.43/min [2460000], rate=52846.40/min [2470000], rate=53042.23/min [2480000], rate=53161.84/min [2490000], rate=53186.19/min [2500000], rate=53210.36/min [2510000], rate=53234.36/min [2520000], rate=53220.70/min [2530000], rate=53281.85/min [2540000], rate=53324.00/min [2550000], rate=53496.50/min [2560000], rate=53650.02/min [2570000], rate=53840.78/min [2580000], rate=54031.41/min [2590000], rate=54203.00/min [2600000], rate=54412.28/min [2610000], rate=54602.51/min [2620000], rate=54792.61/min [2630000], rate=54963.43/min [2640000], rate=55153.20/min [2650000], rate=55323.59/min [2660000], rate=55435.92/min [2670000], rate=55605.69/min [2680000], rate=55794.59/min [2690000], rate=55983.35/min [2700000], rate=56152.51/min [2710000], rate=56243.51/min -building interval tree based on /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=75000.00/min [30000], rate=72000.00/min [40000], rate=48979.59/min [50000], rate=52631.58/min [60000], rate=54545.45/min [70000], rate=60000.00/min [80000], rate=67605.63/min [90000], rate=75000.00/min [100000], rate=82191.78/min [110000], rate=90410.96/min [120000], rate=98630.14/min [130000], rate=105405.41/min [140000], rate=112000.00/min [150000], rate=116883.12/min [160000], rate=124675.32/min [170000], rate=118604.65/min [180000], rate=105882.35/min [190000], rate=111764.71/min [200000], rate=117647.06/min [210000], rate=122330.10/min [220000], rate=120000.00/min [230000], rate=116949.15/min [240000], rate=111627.91/min [250000], rate=107913.67/min [260000], rate=99363.06/min [270000], rate=85263.16/min [280000], rate=87958.12/min [290000], rate=90625.00/min [300000], rate=90909.09/min [310000], rate=91176.47/min [320000], rate=91866.03/min [330000], rate=91244.24/min [340000], rate=91479.82/min [350000], rate=93333.33/min [360000], rate=95154.19/min [370000], rate=96943.23/min [380000], rate=99130.43/min [390000], rate=101739.13/min [400000], rate=103448.28/min [410000], rate=105579.40/min [420000], rate=107692.31/min [430000], rate=109787.23/min [440000], rate=112340.43/min [450000], rate=114893.62/min [460000], rate=116949.15/min [470000], rate=118987.34/min [480000], rate=121518.99/min [490000], rate=124050.63/min [500000], rate=126050.42/min [510000], rate=128033.47/min [520000], rate=130000.00/min [530000], rate=131950.21/min [540000], rate=134439.83/min [550000], rate=135802.47/min [560000], rate=133864.54/min [570000], rate=132558.14/min [580000], rate=131320.75/min [590000], rate=130147.06/min [600000], rate=127208.48/min [610000], rate=126206.90/min [620000], rate=127835.05/min [630000], rate=128571.43/min [640000], rate=129729.73/min [650000], rate=131313.13/min [660000], rate=132885.91/min [670000], rate=134899.33/min [680000], rate=136454.85/min [690000], rate=138461.54/min [700000], rate=140000.00/min [710000], rate=141528.24/min [720000], rate=142574.26/min [730000], rate=141747.57/min [740000], rate=142307.69/min [750000], rate=144230.77/min [760000], rate=145686.90/min [770000], rate=146666.67/min [780000], rate=144444.44/min [790000], rate=140236.69/min [800000], rate=139534.88/min [810000], rate=138857.14/min [820000], rate=137815.13/min [830000], rate=138718.66/min [840000], rate=140000.00/min [850000], rate=138586.96/min [860000], rate=137967.91/min [870000], rate=136649.21/min [880000], rate=135732.65/min [890000], rate=134170.85/min [900000], rate=135000.00/min [910000], rate=135820.90/min [920000], rate=136633.66/min [930000], rate=137777.78/min [940000], rate=138916.26/min [950000], rate=140394.09/min [960000], rate=141523.34/min [970000], rate=142647.06/min [980000], rate=143765.28/min [990000], rate=145232.27/min [1000000], rate=146699.27/min [1010000], rate=147804.88/min [1020000], rate=149268.29/min [1030000], rate=150364.96/min [1040000], rate=151824.82/min [1050000], rate=153284.67/min [1060000], rate=153995.16/min [1070000], rate=155447.94/min [1080000], rate=156521.74/min [1090000], rate=157971.01/min [1100000], rate=158273.38/min [1110000], rate=155244.76/min [1120000], rate=151693.00/min [1130000], rate=149010.99/min [1140000], rate=147732.18/min [1150000], rate=147751.61/min [1160000], rate=146526.32/min [1170000], rate=145341.61/min [1180000], rate=144785.28/min [1190000], rate=145121.95/min [1200000], rate=146044.62/min [1210000], rate=146963.56/min [1220000], rate=147580.65/min [1230000], rate=148790.32/min [1240000], rate=150000.00/min [1250000], rate=150905.43/min [1260000], rate=151807.23/min [1270000], rate=152400.00/min [1280000], rate=153600.00/min [1290000], rate=153876.74/min [1300000], rate=152941.18/min [1310000], rate=154117.65/min [1320000], rate=154990.22/min [1330000], rate=156164.38/min [1340000], rate=155512.57/min [1350000], rate=153409.09/min [1360000], rate=150553.51/min [1370000], rate=150549.45/min [1380000], rate=148920.86/min [1390000], rate=147872.34/min [1400000], rate=148672.57/min [1410000], rate=149206.35/min [1420000], rate=148691.10/min [1430000], rate=148700.17/min [1440000], rate=147692.31/min [1450000], rate=146464.65/min [1460000], rate=146000.00/min [1470000], rate=146511.63/min [1480000], rate=146776.86/min [1490000], rate=147524.75/min [1500000], rate=148270.18/min [1510000], rate=148768.47/min [1520000], rate=148534.20/min [1530000], rate=146645.37/min [1540000], rate=145971.56/min [1550000], rate=145768.03/min [1560000], rate=145116.28/min [1570000], rate=144257.27/min [1580000], rate=143202.42/min [1590000], rate=142388.06/min [1600000], rate=143070.04/min [1610000], rate=143536.40/min [1620000], rate=144213.65/min [1630000], rate=144888.89/min [1640000], rate=145562.13/min [1650000], rate=146449.70/min [1660000], rate=147337.28/min [1670000], rate=148005.91/min [1680000], rate=148672.57/min [1690000], rate=149337.26/min [1700000], rate=149341.14/min [1710000], rate=148911.47/min [1720000], rate=149565.22/min [1730000], rate=150217.08/min [1740000], rate=151085.38/min [1750000], rate=151296.83/min [1760000], rate=150427.35/min [1770000], rate=147910.86/min [1780000], rate=148127.60/min [1790000], rate=148137.93/min [1800000], rate=144578.31/min [1810000], rate=144414.89/min [1820000], rate=145019.92/min [1830000], rate=143529.41/min [1840000], rate=143376.62/min [1850000], rate=142673.52/min [1860000], rate=142346.94/min [1870000], rate=142025.32/min [1880000], rate=142424.24/min [1890000], rate=143001.26/min [1900000], rate=143576.83/min [1910000], rate=144150.94/min [1920000], rate=144723.62/min [1930000], rate=144931.16/min [1940000], rate=138736.59/min [1950000], rate=127450.98/min [1960000], rate=120122.57/min [1970000], rate=114980.54/min [1980000], rate=109191.18/min [1990000], rate=103826.09/min [2000000], rate=99173.55/min [2010000], rate=95185.48/min [2020000], rate=91471.70/min [2030000], rate=87878.79/min [2040000], rate=84764.54/min [2050000], rate=81945.37/min [2060000], rate=79129.32/min [2070000], rate=76336.82/min [2080000], rate=73628.32/min [2090000], rate=71780.19/min [2100000], rate=70116.86/min [2110000], rate=68174.47/min [2120000], rate=66841.83/min [2130000], rate=65304.04/min [2140000], rate=63912.39/min [2150000], rate=62804.28/min [2160000], rate=61773.12/min [2170000], rate=60642.76/min [2180000], rate=59671.53/min [2190000], rate=58556.15/min [2200000], rate=57768.05/min [2210000], rate=57032.26/min [2220000], rate=56345.18/min [2230000], rate=55796.50/min [2240000], rate=55172.41/min [2250000], rate=54766.73/min [2260000], rate=54370.49/min [2270000], rate=54026.18/min [2280000], rate=53731.34/min [2290000], rate=53421.46/min [2300000], rate=53097.35/min [2310000], rate=52800.00/min [2320000], rate=52528.30/min [2330000], rate=52222.64/min [2340000], rate=52077.15/min [2350000], rate=51914.58/min [2360000], rate=51716.58/min [2370000], rate=51540.41/min [2380000], rate=51422.40/min [2390000], rate=51305.90/min [2400000], rate=51245.55/min [2410000], rate=51077.36/min [2420000], rate=50965.25/min [2430000], rate=50925.60/min [2440000], rate=50904.03/min [2450000], rate=50794.75/min [2460000], 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rate=34763.48/min [1590000], rate=34716.16/min [1600000], rate=34657.04/min [1610000], rate=34648.49/min [1620000], rate=34751.52/min [1630000], rate=34754.80/min [1640000], rate=34844.19/min [1650000], rate=34883.72/min [1660000], rate=34935.11/min [1670000], rate=35010.48/min [1680000], rate=35024.32/min [1690000], rate=35025.91/min [1700000], rate=35063.60/min [1710000], rate=35112.94/min [1720000], rate=35209.83/min [1730000], rate=35306.12/min [1740000], rate=35353.88/min [1750000], rate=35365.44/min [1760000], rate=35436.24/min [1770000], rate=35470.94/min [1780000], rate=35576.28/min [1790000], rate=35633.71/min [1800000], rate=35620.05/min [1810000], rate=35735.44/min [1820000], rate=35779.82/min [1830000], rate=35858.92/min [1840000], rate=35902.44/min [1850000], rate=35992.22/min [1860000], rate=36081.47/min [1870000], rate=36158.56/min [1880000], rate=36258.44/min [1890000], rate=36311.24/min [1900000], rate=36375.24/min [1910000], rate=36485.20/min [1920000], rate=36559.82/min [1930000], rate=36633.98/min [1940000], rate=36696.09/min [1950000], rate=36769.33/min [1960000], rate=36865.20/min [1970000], rate=36949.05/min [1980000], rate=37032.42/min [1990000], rate=37138.41/min [2000000], rate=37232.39/min [2010000], rate=37325.91/min [2020000], rate=37430.51/min [2030000], rate=37546.24/min [2040000], rate=37673.13/min [2050000], rate=37776.41/min [2060000], rate=37902.48/min [2070000], rate=38004.90/min [2080000], rate=38141.81/min [2090000], rate=38278.39/min [2100000], rate=38402.93/min [2110000], rate=38527.08/min [2120000], rate=38557.14/min [2130000], rate=38505.57/min [2140000], rate=38477.67/min [2150000], rate=38495.97/min [2160000], rate=38491.24/min [2170000], rate=38520.71/min [2180000], rate=38538.60/min [2190000], rate=38578.98/min [2200000], rate=38641.69/min [2210000], rate=38681.45/min [2220000], rate=38709.68/min [2230000], rate=38748.91/min [2240000], rate=38776.69/min [2250000], rate=38826.57/min [2260000], rate=38887.30/min [2270000], rate=38936.54/min [2280000], rate=38985.47/min [2290000], rate=39023.00/min [2300000], rate=39093.48/min [2310000], rate=39174.67/min [2320000], rate=39244.43/min [2330000], rate=39313.84/min [2340000], rate=39371.85/min [2350000], rate=39429.53/min [2360000], rate=39519.96/min [2370000], rate=39576.96/min [2380000], rate=39644.64/min [2390000], rate=39711.99/min [2400000], rate=39801.00/min [2410000], rate=39878.65/min [2420000], rate=40000.00/min [2430000], rate=40099.01/min [2440000], rate=40186.66/min [2450000], rate=40251.92/min [2460000], rate=40349.92/min [2470000], rate=40414.51/min [2480000], rate=40489.80/min [2490000], rate=40575.77/min [2500000], rate=40661.43/min [2510000], rate=40735.73/min [2520000], rate=40831.76/min [2530000], rate=40927.47/min [2540000], rate=41000.81/min [2550000], rate=41095.89/min [2560000], rate=41179.62/min [2570000], rate=41240.97/min [2580000], rate=41313.05/min [2590000], rate=41395.84/min [2600000], rate=41467.30/min [2610000], rate=41527.45/min [2620000], rate=41609.32/min [2630000], rate=41679.87/min [2640000], rate=41750.13/min [2650000], rate=41820.09/min [2660000], rate=41878.77/min [2670000], rate=41937.17/min [2680000], rate=42006.27/min [2690000], rate=42086.05/min [2700000], rate=42154.57/min [2710000], rate=42222.80/min [2720000], rate=43404.26/min [2730000], rate=43540.67/min [2740000], rate=43688.55/min [2750000], rate=43836.34/min [2760000], rate=43949.04/min [2770000], rate=44049.83/min [2780000], rate=44173.73/min [2790000], rate=44274.00/min [2800000], rate=44385.73/min [2810000], rate=44485.49/min [2820000], rate=44596.73/min [2830000], rate=44707.74/min [2840000], rate=44830.31/min [2850000], rate=44929.06/min [2860000], rate=45003.93/min [2870000], rate=45078.53/min [2880000], rate=45152.86/min [2890000], rate=45238.72/min [2900000], rate=45312.50/min [2910000], rate=45386.02/min [2920000], rate=45506.49/min [2930000], rate=45626.78/min [2940000], rate=45758.75/min [2950000], rate=45890.59/min [2960000], rate=46010.36/min [2970000], rate=46129.95/min [2980000], rate=46249.35/min [2990000], rate=46356.59/min [3000000], rate=46475.60/min [3010000], rate=46582.41/min [3020000], rate=46652.94/min [3030000], rate=46711.20/min [3040000], rate=46781.23/min [3050000], rate=46863.00/min [3060000], rate=46932.52/min [3070000], rate=47013.78/min [3080000], rate=47106.81/min [3090000], rate=47187.58/min [3100000], rate=47268.11/min [3110000], rate=47348.39/min [3120000], rate=47440.45/min [3130000], rate=47520.24/min [3140000], rate=47611.83/min [3150000], rate=47703.18/min [3160000], rate=47794.30/min [3170000], rate=47885.20/min [3180000], rate=47975.86/min [3190000], rate=48078.37/min [3200000], rate=48180.68/min [3210000], rate=48307.00/min [3220000], rate=48445.34/min [3230000], rate=48571.43/min [3240000], rate=48685.20/min [3250000], rate=48798.80/min [3260000], rate=48900.00/min [3270000], rate=48988.76/min [3280000], rate=49077.31/min [3290000], rate=49177.88/min [3300000], rate=49265.99/min [3310000], rate=49366.14/min [3320000], rate=49453.82/min [2720000], rate=42312.68/min [2730000], rate=42391.30/min [2740000], rate=42480.62/min [2750000], rate=42569.66/min [2760000], rate=42669.42/min [2770000], rate=42757.91/min [2780000], rate=42857.14/min [2790000], rate=42945.10/min [2800000], rate=43032.79/min [2810000], rate=43142.27/min [2820000], rate=43240.48/min [2830000], rate=43338.44/min [2840000], rate=43447.22/min [2850000], rate=43555.78/min [2860000], rate=43686.35/min [2870000], rate=43783.37/min [2880000], rate=43880.14/min [2890000], rate=43998.99/min [2900000], rate=44095.29/min [2910000], rate=44213.72/min [2920000], rate=44343.20/min [2930000], rate=44472.55/min [2940000], rate=44601.77/min [2950000], rate=44742.16/min [2960000], rate=44882.49/min [2970000], rate=45022.74/min [2980000], rate=45151.52/min [2990000], rate=45280.16/min [3000000], rate=45385.78/min [3010000], rate=45479.73/min [3020000], rate=45573.44/min [3030000], rate=45678.39/min [3040000], rate=45771.64/min [3050000], rate=45876.16/min [3060000], rate=45968.95/min [3070000], rate=46073.04/min [3080000], rate=46176.91/min [3090000], rate=46269.03/min [3100000], rate=46303.21/min [3110000], rate=46314.22/min [3120000], rate=46371.07/min [3130000], rate=46404.74/min [3140000], rate=46438.25/min [3150000], rate=46460.18/min [3160000], rate=46504.78/min [3170000], rate=46526.42/min [3180000], rate=46570.66/min [3190000], rate=46603.36/min [3200000], rate=46658.57/min [3210000], rate=46690.91/min [3220000], rate=46700.51/min [3230000], rate=46755.13/min [3240000], rate=46843.37/min [3250000], rate=46886.27/min [3260000], rate=46906.47/min [3270000], rate=46949.03/min [3280000], rate=46991.40/min [3290000], rate=47022.39/min [3300000], rate=47053.23/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir --filt_file /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 0.00 reads per min processed... 12000000.00 reads per min processed... 18000000.00 reads per min processed... 12000000.00 reads per min processed... 15000000.00 reads per min processed... 12000000.00 reads per min processed... 14000000.00 reads per min processed... 12000000.00 reads per min processed... 13500000.00 reads per min processed... 12000000.00 reads per min processed... 13200000.00 reads per min processed... 12000000.00 reads per min processed... 13000000.00 reads per min processed... 12000000.00 reads per min processed... 11250000.00 reads per min processed... 12000000.00 reads per min processed... 11333333.33 reads per min processed... 12000000.00 reads per min processed... 11400000.00 reads per min processed... 10000000.00 reads per min processed... 9692307.69 reads per min processed... 8800000.00 reads per min processed... 8625000.00 reads per min processed... 8000000.00 reads per min processed... 7894736.84 reads per min processed... 7800000.00 reads per min processed... 7714285.71 reads per min processed... 7304347.83 reads per min processed... 7250000.00 reads per min processed... 7200000.00 reads per min processed... 7153846.15 reads per min processed... 6857142.86 reads per min processed... 6827586.21 reads per min processed... 6800000.00 reads per min processed... 6562500.00 reads per min processed... 6545454.55 reads per min processed... 6529411.76 reads per min processed... 6514285.71 reads per min processed... 6324324.32 reads per min processed... 6315789.47 reads per min processed... 6307692.31 reads per min processed... 6300000.00 reads per min processed... 6142857.14 reads per min processed... 5866666.67 reads per min processed... 5869565.22 reads per min processed... 5750000.00 reads per min processed... 5755102.04 reads per min processed... 5647058.82 reads per min processed... 5653846.15 reads per min processed... 5660377.36 reads per min processed... 5563636.36 reads per min processed... 5571428.57 reads per min processed... 5578947.37 reads per min processed... 5491525.42 reads per min processed... 5593220.34 reads per min processed... 5600000.00 reads per min processed... 5516129.03 reads per min processed... 5523809.52 reads per min processed... 5531250.00 reads per min processed... 5454545.45 reads per min processed... 5462686.57 reads per min processed... 5470588.24 reads per min processed... 5478260.87 reads per min processed... 5485714.29 reads per min processed... 5492957.75 reads per min processed... 5500000.00 reads per min processed... 5432432.43 reads per min processed... 5440000.00 reads per min processed... 5520000.00 reads per min processed... 5526315.79 reads per min processed... 5605263.16 reads per min processed... 5610389.61 reads per min processed... 5688311.69 reads per min processed... 5692307.69 reads per min processed... 5696202.53 reads per min processed... 5772151.90 reads per min processed... 5775000.00 reads per min processed... 5850000.00 reads per min processed... 5851851.85 reads per min processed... 5925925.93 reads per min processed... 5926829.27 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 5931818.18 reads per min processed... 5932584.27 reads per min processed... 5933333.33 reads per min processed... 5934065.93 reads per min processed... 5934782.61 reads per min processed... 5935483.87 reads per min processed... 5936170.21 reads per min processed... 5875000.00 reads per min processed... 5876288.66 reads per min processed... 5877551.02 reads per min processed... 5878787.88 reads per min processed... 5821782.18 reads per min processed... 5881188.12 reads per min processed... 5825242.72 reads per min processed... 5826923.08 reads per min processed... 5828571.43 reads per min processed... 5830188.68 reads per min processed... 5777777.78 reads per min processed... 5779816.51 reads per min processed... 5781818.18 reads per min processed... 5783783.78 reads per min processed... 5785714.29 reads per min processed... 5787610.62 reads per min processed... 5789473.68 reads per min processed... 5791304.35 reads per min processed... 5793103.45 reads per min processed... 5794871.79 reads per min processed... 5796610.17 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.lT9KTs8yqN/EndoN_FFPE_L06_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.lT9KTs8yqN/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -185535.412371 EM: Round [1] log likelihood: -185124.113175 EM: Round [2] log likelihood: -184968.838502 EM: Round [3] log likelihood: -184895.979050 EM: Round [4] log likelihood: -184858.046861 EM: Round [5] log likelihood: -184836.950656 EM: Round [6] log likelihood: -184824.558628 EM: Round [7] log likelihood: -184816.901891 EM: Round [8] log likelihood: -184811.945174 EM: Round [9] log likelihood: -184808.600339 EM: Round [10] log likelihood: -184806.260687 EM: Round [11] log likelihood: -184804.573305 EM: Round [12] log likelihood: -184803.324319 EM: Round [13] log likelihood: -184802.379098 EM: Round [14] log likelihood: -184801.649942 EM: Round [15] log likelihood: -184801.077978 EM: Round [16] log likelihood: -184800.622630 EM: Round [17] log likelihood: -184800.255294 EM: Round [18] log likelihood: -184799.955397 EM: Round [19] log likelihood: -184799.707892 EM: Round [20] log likelihood: -184799.501595 EM: Round [21] log likelihood: -184799.328085 EM: Round [22] log likelihood: -184799.180939 EM: Round [23] log likelihood: -184799.055203 EM: Round [24] log likelihood: -184798.947012 EM: Round [25] log likelihood: -184798.853324 EM: Round [26] log likelihood: -184798.771721 EM: Round [27] log likelihood: -184798.700263 EM: Round [28] log likelihood: -184798.637383 EM: Round [29] log likelihood: -184798.581800 EM: Round [30] log likelihood: -184798.532467 EM: Round [31] log likelihood: -184798.488513 EM: Round [32] log likelihood: -184798.449216 EM: Round [33] log likelihood: -184798.413970 EM: Round [34] log likelihood: -184798.382264 EM: Round [35] log likelihood: -184798.353664 EM: Round [36] log likelihood: -184798.327801 EM: Round [37] log likelihood: -184798.304358 EM: Round [38] log likelihood: -184798.283062 EM: Round [39] log likelihood: -184798.263677 EM: Round [40] log likelihood: -184798.245999 EM: Round [41] log likelihood: -184798.229848 EM: Round [42] log likelihood: -184798.215068 EM: Round [43] log likelihood: -184798.201521 EM: Round [44] log likelihood: -184798.189086 EM: Round [45] log likelihood: -184798.177655 EM: Round [46] log likelihood: -184798.167133 EM: Round [47] log likelihood: -184798.157436 EM: Round [48] log likelihood: -184798.148487 EM: Round [49] log likelihood: -184798.140220 EM: Round [50] log likelihood: -184798.132574 EM: Round [51] log likelihood: -184798.125494 EM: Round [52] log likelihood: -184798.118932 EM: Round [53] log likelihood: -184798.112844 EM: Round [54] log likelihood: -184798.107189 EM: Round [55] log likelihood: -184798.101932 EM: Round [56] log likelihood: -184798.097041 EM: Round [57] log likelihood: -184798.092485 EM: Round [58] log likelihood: -184798.088237 EM: Round [59] log likelihood: -184798.084275 EM: Round [60] log likelihood: -184798.080574 EM: Round [61] log likelihood: -184798.077115 EM: Round [62] log likelihood: -184798.073880 EM: Round [63] log likelihood: -184798.070851 EM: Round [64] log likelihood: -184798.068013 EM: Round [65] log likelihood: -184798.065351 EM: Round [66] log likelihood: -184798.062854 EM: Round [67] log likelihood: -184798.060509 EM: Round [68] log likelihood: -184798.058304 EM: Round [69] log likelihood: -184798.056231 EM: Round [70] log likelihood: -184798.054279 EM: Round [71] log likelihood: -184798.052440 EM: Round [72] log likelihood: -184798.050707 EM: Round [73] log likelihood: -184798.049072 EM: Round [74] log likelihood: -184798.047528 EM: Round [75] log likelihood: -184798.046070 EM: Round [76] log likelihood: -184798.044692 EM: Round [77] log likelihood: -184798.043387 EM: Round [78] log likelihood: -184798.042153 EM: Round [79] log likelihood: -184798.040984 EM: Round [80] log likelihood: -184798.039875 EM: Round [81] log likelihood: -184798.038824 EM: Round [82] log likelihood: -184798.037826 EM: Round [83] log likelihood: -184798.036878 EM: Round [84] log likelihood: -184798.035977 EM: Round [85] log likelihood: -184798.035121 EM: Round [86] log likelihood: -184798.034306 EM: Round [87] log likelihood: -184798.033530 EM: Round [88] log likelihood: -184798.032791 EM: Round [89] log likelihood: -184798.032087 EM: Round [90] log likelihood: -184798.031415 EM: Round [91] log likelihood: -184798.030774 EM: Round [92] log likelihood: -184798.030162 EM: Round [93] log likelihood: -184798.029578 EM: Round [94] log likelihood: -184798.029019 EM: Round [95] log likelihood: -184798.028484 EM: Round [96] log likelihood: -184798.027973 EM: Round [97] log likelihood: -184798.027484 EM: Round [98] log likelihood: -184798.027015 EM: Round [99] log likelihood: -184798.026566 EM: Round [100] log likelihood: -184798.026135 EM: Round [101] log likelihood: -184798.025722 EM: Round [102] log likelihood: -184798.025326 EM: Round [103] log likelihood: -184798.024945 EM: Round [104] log likelihood: -184798.024580 EM: Round [105] log likelihood: -184798.024229 EM: Round [106] log likelihood: -184798.023891 EM: Round [107] log likelihood: -184798.023567 EM: Round [108] log likelihood: -184798.023255 EM: Round [109] log likelihood: -184798.022954 EM: Round [110] log likelihood: -184798.022665 EM: Round [111] log likelihood: -184798.022386 EM: Round [112] log likelihood: -184798.022118 EM: Round [113] log likelihood: -184798.021859 EM: Round [114] log likelihood: -184798.021609 EM: Round [115] log likelihood: -184798.021369 EM: Round [116] log likelihood: -184798.021136 EM: Round [117] log likelihood: -184798.020912 EM: Round [118] log likelihood: -184798.020695 EM: Round [119] log likelihood: -184798.020486 EM: Round [120] log likelihood: -184798.020284 EM: Round [121] log likelihood: -184798.020089 EM: Round [122] log likelihood: -184798.019900 EM: Round [123] log likelihood: -184798.019717 EM: Round [124] log likelihood: -184798.019541 EM: Round [125] log likelihood: -184798.019369 EM: Round [126] log likelihood: -184798.019204 EM: Round [127] log likelihood: -184798.019044 EM: Round [128] log likelihood: -184798.018888 EM: Round [129] log likelihood: -184798.018738 EM: Round [130] log likelihood: -184798.018592 EM: Round [131] log likelihood: -184798.018451 EM: Round [132] log likelihood: -184798.018314 EM: Round [133] log likelihood: -184798.018181 EM: Round [134] log likelihood: -184798.018052 EM: Round [135] log likelihood: -184798.017927 EM: Round [136] log likelihood: -184798.017805 EM: Round [137] log likelihood: -184798.017688 EM: Round [138] log likelihood: -184798.017573 EM: Round [139] log likelihood: -184798.017462 EM: Round [140] log likelihood: -184798.017354 EM: Round [141] log likelihood: -184798.017249 EM: Round [142] log likelihood: -184798.017147 EM: Round [143] log likelihood: -184798.017048 EM: Stopping iterations at round 143 due to insufficient improvement in likelihood. EM: Starting log likelihood: -185299.688347 EM: Round [1] log likelihood: -184940.867854 EM: Round [2] log likelihood: -184812.537424 EM: Round [3] log likelihood: -184754.082775 EM: Round [4] log likelihood: -184724.243345 EM: Round [5] log likelihood: -184707.937107 EM: Round [6] log likelihood: -184698.529548 EM: Round [7] log likelihood: -184692.823447 EM: Round [8] log likelihood: -184689.197313 EM: Round [9] log likelihood: -184686.794594 EM: Round [10] log likelihood: -184685.143905 EM: Round [11] log likelihood: -184683.974645 EM: Round [12] log likelihood: -184683.124848 EM: Round [13] log likelihood: -184682.493681 EM: Round [14] log likelihood: -184682.016100 EM: Round [15] log likelihood: -184681.648816 EM: Round [16] log likelihood: -184681.362243 EM: Round [17] log likelihood: -184681.135698 EM: Round [18] log likelihood: -184680.954441 EM: Round [19] log likelihood: -184680.807796 EM: Round [20] log likelihood: -184680.687919 EM: Round [21] log likelihood: -184680.588974 EM: Round [22] log likelihood: -184680.506568 EM: Round [23] log likelihood: -184680.437359 EM: Round [24] log likelihood: -184680.378780 EM: Round [25] log likelihood: -184680.328839 EM: Round [26] log likelihood: -184680.285975 EM: Round [27] log likelihood: -184680.248959 EM: Round [28] log likelihood: -184680.216809 EM: Round [29] log likelihood: -184680.188738 EM: Round [30] log likelihood: -184680.164108 EM: Round [31] log likelihood: -184680.142400 EM: Round [32] log likelihood: -184680.123186 EM: Round [33] log likelihood: -184680.106114 EM: Round [34] log likelihood: -184680.090891 EM: Round [35] log likelihood: -184680.077270 EM: Round [36] log likelihood: -184680.065045 EM: Round [37] log likelihood: -184680.054040 EM: Round [38] log likelihood: -184680.044107 EM: Round [39] log likelihood: -184680.035118 EM: Round [40] log likelihood: -184680.026962 EM: Round [41] log likelihood: -184680.019546 EM: Round [42] log likelihood: -184680.012788 EM: Round [43] log likelihood: -184680.006617 EM: Round [44] log likelihood: -184680.000970 EM: Round [45] log likelihood: -184679.995794 EM: Round [46] log likelihood: -184679.991039 EM: Round [47] log likelihood: -184679.986665 EM: Round [48] log likelihood: -184679.982634 EM: Round [49] log likelihood: -184679.978913 EM: Round [50] log likelihood: -184679.975473 EM: Round [51] log likelihood: -184679.972287 EM: Round [52] log likelihood: -184679.969334 EM: Round [53] log likelihood: -184679.966591 EM: Round [54] log likelihood: -184679.964040 EM: Round [55] log likelihood: -184679.961665 EM: Round [56] log likelihood: -184679.959451 EM: Round [57] log likelihood: -184679.957384 EM: Round [58] log likelihood: -184679.955452 EM: Round [59] log likelihood: -184679.953643 EM: Round [60] log likelihood: -184679.951949 EM: Round [61] log likelihood: -184679.950360 EM: Round [62] log likelihood: -184679.948867 EM: Round [63] log likelihood: -184679.947464 EM: Round [64] log likelihood: -184679.946143 EM: Round [65] log likelihood: -184679.944899 EM: Round [66] log likelihood: -184679.943725 EM: Round [67] log likelihood: -184679.942617 EM: Round [68] log likelihood: -184679.941571 EM: Round [69] log likelihood: -184679.940580 EM: Round [70] log likelihood: -184679.939643 EM: Round [71] log likelihood: -184679.938754 EM: Round [72] log likelihood: -184679.937912 EM: Round [73] log likelihood: -184679.937112 EM: Round [74] log likelihood: -184679.936352 EM: Round [75] log likelihood: -184679.935630 EM: Round [76] log likelihood: -184679.934942 EM: Round [77] log likelihood: -184679.934287 EM: Round [78] log likelihood: -184679.933663 EM: Round [79] log likelihood: -184679.933068 EM: Round [80] log likelihood: -184679.932500 EM: Round [81] log likelihood: -184679.931958 EM: Round [82] log likelihood: -184679.931440 EM: Round [83] log likelihood: -184679.930944 EM: Round [84] log likelihood: -184679.930470 EM: Round [85] log likelihood: -184679.930015 EM: Round [86] log likelihood: -184679.929580 EM: Round [87] log likelihood: -184679.929163 EM: Round [88] log likelihood: -184679.928763 EM: Round [89] log likelihood: -184679.928380 EM: Round [90] log likelihood: -184679.928011 EM: Round [91] log likelihood: -184679.927657 EM: Round [92] log likelihood: -184679.927317 EM: Round [93] log likelihood: -184679.926990 EM: Round [94] log likelihood: -184679.926675 EM: Round [95] log likelihood: -184679.926372 EM: Round [96] log likelihood: -184679.926080 EM: Round [97] log likelihood: -184679.925799 EM: Round [98] log likelihood: -184679.925529 EM: Round [99] log likelihood: -184679.925268 EM: Round [100] log likelihood: -184679.925016 EM: Round [101] log likelihood: -184679.924774 EM: Round [102] log likelihood: -184679.924539 EM: Round [103] log likelihood: -184679.924313 EM: Round [104] log likelihood: -184679.924095 EM: Round [105] log likelihood: -184679.923884 EM: Round [106] log likelihood: -184679.923680 EM: Round [107] log likelihood: -184679.923483 EM: Round [108] log likelihood: -184679.923292 EM: Round [109] log likelihood: -184679.923108 EM: Round [110] log likelihood: -184679.922929 EM: Round [111] log likelihood: -184679.922757 EM: Round [112] log likelihood: -184679.922589 EM: Round [113] log likelihood: -184679.922428 EM: Round [114] log likelihood: -184679.922271 EM: Round [115] log likelihood: -184679.922119 EM: Round [116] log likelihood: -184679.921972 EM: Round [117] log likelihood: -184679.921829 EM: Round [118] log likelihood: -184679.921691 EM: Round [119] log likelihood: -184679.921557 EM: Round [120] log likelihood: -184679.921426 EM: Round [121] log likelihood: -184679.921300 EM: Round [122] log likelihood: -184679.921178 EM: Round [123] log likelihood: -184679.921059 EM: Round [124] log likelihood: -184679.920943 EM: Round [125] log likelihood: -184679.920831 EM: Round [126] log likelihood: -184679.920722 EM: Round [127] log likelihood: -184679.920616 EM: Round [128] log likelihood: -184679.920514 EM: Round [129] log likelihood: -184679.920414 EM: Stopping iterations at round 129 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 211551416 > /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir > /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir --annotate /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir -done, see /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 868, filtered: 7913) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000239268.3] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000239556.4] WARNING, no entry stored in dbm for [ENSG00000227681.5] WARNING, no entry stored in dbm for [ENSG00000230490.3] 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 [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000251532.1] WARNING, no entry stored in dbm for [ENSG00000281691.1] WARNING, no entry stored in dbm for [ENSG00000229770.2] WARNING, no entry stored in dbm for [ENSG00000225851.1] WARNING, no entry stored in dbm for [ENSG00000198237.8] WARNING, no entry stored in dbm for [ENSG00000168405.17] WARNING, no entry stored in dbm for [ENSG00000267532.5] WARNING, no entry stored in dbm for [ENSG00000188511.12] WARNING, no entry stored in dbm for [ENSG00000239556.4] WARNING, no entry stored in dbm for [ENSG00000185710.9] WARNING, no entry stored in dbm for [ENSG00000284740.1] WARNING, no entry stored in dbm for [ENSG00000257252.6] WARNING, no entry stored in dbm for [ENSG00000217801.10] WARNING, no entry stored in dbm for [ENSG00000248551.1] WARNING, no entry stored in dbm for [ENSG00000286494.1] WARNING, no entry stored in dbm for [ENSG00000239268.3] WARNING, no entry stored in dbm for [ENSG00000276538.1] WARNING, no entry stored in dbm for [ENSG00000243024.6] WARNING, no entry stored in dbm for [ENSG00000248015.7] 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 [ENSG00000260689.2] WARNING, no entry stored in dbm for [ENSG00000225594.1] WARNING, no entry stored in dbm for [ENSG00000285810.1] WARNING, no entry stored in dbm for [ENSG00000239224.3] WARNING, no entry stored in dbm for [ENSG00000235145.2] WARNING, no entry stored in dbm for [ENSG00000227517.7] WARNING, no entry stored in dbm for [ENSG00000249541.1] WARNING, no entry stored in dbm for [ENSG00000205940.8] WARNING, no entry stored in dbm for [ENSG00000234638.1] WARNING, no entry stored in dbm for [ENSG00000259663.2] WARNING, no entry stored in dbm for [ENSG00000259327.1] WARNING, no entry stored in dbm for [ENSG00000233405.2] WARNING, no entry stored in dbm for [ENSG00000225470.8] WARNING, no entry stored in dbm for [ENSG00000286116.1] WARNING, no entry stored in dbm for [ENSG00000286742.1] WARNING, no entry stored in dbm for [ENSG00000270576.1] WARNING, no entry stored in dbm for [ENSG00000286607.1] WARNING, no entry stored in dbm for [ENSG00000229950.1] WARNING, no entry stored in dbm for [ENSG00000267750.6] WARNING, no entry stored in dbm for [ENSG00000235530.7] WARNING, no entry stored in dbm for [ENSG00000287299.1] WARNING, no entry stored in dbm for [ENSG00000261670.1] WARNING, no entry stored in dbm for [ENSG00000215448.3] WARNING, no entry stored in dbm for [ENSG00000275465.7] WARNING, no entry stored in dbm for [ENSG00000175061.18] WARNING, no entry stored in dbm for [ENSG00000251676.2] WARNING, no entry stored in dbm for [ENSG00000251676.2] WARNING, no entry stored in dbm for [ENSG00000248826.2] WARNING, no entry stored in dbm for [ENSG00000272078.1] WARNING, no entry stored in dbm for [ENSG00000224391.1] WARNING, no entry stored in dbm for [ENSG00000287400.1] WARNING, no entry stored in dbm for [ENSG00000180747.15] WARNING, no entry stored in dbm for [ENSG00000228948.2] WARNING, no entry stored in dbm for [ENSG00000232724.1] WARNING, no entry stored in dbm for [ENSG00000259278.2] WARNING, no entry stored in dbm for [ENSG00000284986.1] WARNING, no entry stored in dbm for [ENSG00000188002.10] WARNING, no entry stored in dbm for [ENSG00000227681.5] WARNING, no entry stored in dbm for [ENSG00000197301.7] WARNING, no entry stored in dbm for [ENSG00000225482.1] WARNING, no entry stored in dbm for [ENSG00000238069.1] WARNING, no entry stored in dbm for [ENSG00000244705.1] WARNING, no entry stored in dbm for [ENSG00000184139.8] WARNING, no entry stored in dbm for [ENSG00000215869.4] WARNING, no entry stored in dbm for [ENSG00000257074.3] WARNING, no entry stored in dbm for [ENSG00000241030.1] WARNING, no entry stored in dbm for [ENSG00000241286.2] WARNING, no entry stored in dbm for [ENSG00000229700.1] WARNING, no entry stored in dbm for [ENSG00000241081.1] WARNING, no entry stored in dbm for [ENSG00000225483.1] WARNING, no entry stored in dbm for [ENSG00000213935.3] WARNING, no entry stored in dbm for [ENSG00000213653.4] 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 [ENSG00000218716.1] WARNING, no entry stored in dbm for [ENSG00000288015.1] WARNING, no entry stored in dbm for [ENSG00000125804.14] WARNING, no entry stored in dbm for [ENSG00000199415.1] WARNING, no entry stored in dbm for [ENSG00000239437.3] WARNING, no entry stored in dbm for [ENSG00000243373.3] WARNING, no entry stored in dbm for [ENSG00000222976.1] WARNING, no entry stored in dbm for [ENSG00000222826.1] WARNING, no entry stored in dbm for [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000200708.1] WARNING, no entry stored in dbm for [ENSG00000201533.1] WARNING, no entry stored in dbm for [ENSG00000222826.1] WARNING, no entry stored in dbm for [ENSG00000202512.1] WARNING, no entry stored in dbm for [ENSG00000222826.1] WARNING, no entry stored in dbm for [ENSG00000222974.1] WARNING, no entry stored in dbm for [ENSG00000222826.1] WARNING, no entry stored in dbm for [ENSG00000202351.1] WARNING, no entry stored in dbm for [ENSG00000222826.1] WARNING, no entry stored in dbm for [ENSG00000200783.1] WARNING, no entry stored in dbm for [ENSG00000222826.1] WARNING, no entry stored in dbm for [ENSG00000222240.1] WARNING, no entry stored in dbm for [ENSG00000201201.1] WARNING, no entry stored in dbm for [ENSG00000279905.1] WARNING, no entry stored in dbm for [ENSG00000260807.7] WARNING, no entry stored in dbm for [ENSG00000272168.8] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000251209.9] WARNING, no entry stored in dbm for [ENSG00000227038.3] WARNING, no entry stored in dbm for [ENSG00000225778.5] WARNING, no entry stored in dbm for [ENSG00000099725.14] WARNING, no entry stored in dbm for [ENSG00000245466.1] WARNING, no entry stored in dbm for [ENSG00000261122.6] WARNING, no entry stored in dbm for [ENSG00000284738.1] WARNING, no entry stored in dbm for [ENSG00000200966.1] WARNING, no entry stored in dbm for [ENSG00000222826.1] WARNING, no entry stored in dbm for [ENSG00000244257.5] WARNING, no entry stored in dbm for [ENSG00000224812.3] WARNING, no entry stored in dbm for [ENSG00000279491.1] WARNING, no entry stored in dbm for [ENSG00000166104.15] WARNING, no entry stored in dbm for [ENSG00000273125.2] WARNING, no entry stored in dbm for [ENSG00000224914.4] WARNING, no entry stored in dbm for [ENSG00000189223.15] WARNING, no entry stored in dbm for [ENSG00000246211.2] WARNING, no entry stored in dbm for [ENSG00000286960.1] WARNING, no entry stored in dbm for [ENSG00000257135.7] WARNING, no entry stored in dbm for 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entry stored in dbm for [ENSG00000240708.2] WARNING, no entry stored in dbm for [ENSG00000230785.2] WARNING, no entry stored in dbm for [ENSG00000231929.2] WARNING, no entry stored in dbm for [ENSG00000206341.7] WARNING, no entry stored in dbm for [ENSG00000233606.2] WARNING, no entry stored in dbm for [ENSG00000233606.2] WARNING, no entry stored in dbm for [ENSG00000276476.3] WARNING, no entry stored in dbm for [ENSG00000261404.7] WARNING, no entry stored in dbm for [ENSG00000261404.7] WARNING, no entry stored in dbm for [ENSG00000279036.1] WARNING, no entry stored in dbm for [ENSG00000272645.3] WARNING, no entry stored in dbm for [ENSG00000251842.1] WARNING, no entry stored in dbm for [ENSG00000239533.6] WARNING, no entry stored in dbm for [ENSG00000281103.2] WARNING, no entry stored in dbm for [ENSG00000215333.3] WARNING, no entry stored in dbm for [ENSG00000257915.1] WARNING, no entry stored in dbm for [ENSG00000259905.7] WARNING, no entry stored in dbm for [ENSG00000272396.1] WARNING, no entry stored in dbm for [ENSG00000229236.3] WARNING, no entry stored in dbm for [ENSG00000281196.1] WARNING, no entry stored in dbm for [ENSG00000214185.3] WARNING, no entry stored in dbm for [ENSG00000228876.4] WARNING, no entry stored in dbm for [ENSG00000275340.1] WARNING, no entry stored in dbm for [ENSG00000275340.1] WARNING, no entry stored in dbm for [ENSG00000235726.7] WARNING, no entry stored in dbm for [ENSG00000269680.1] WARNING, no entry stored in dbm for [ENSG00000230869.1] WARNING, no entry stored in dbm for [ENSG00000255052.5] WARNING, no entry stored in dbm for [ENSG00000254016.3] WARNING, no entry stored in dbm for [ENSG00000215908.10] WARNING, no entry stored in dbm for [ENSG00000236438.7] WARNING, no entry stored in dbm for [ENSG00000249966.1] WARNING, no entry stored in dbm for [ENSG00000179840.5] WARNING, no entry stored in dbm for [ENSG00000269486.2] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000226688.7] WARNING, no entry stored in dbm for [ENSG00000233098.9] WARNING, no entry stored in dbm for [ENSG00000215016.2] WARNING, no entry stored in dbm for [ENSG00000258980.1] WARNING, no entry stored in dbm for [ENSG00000287891.1] WARNING, no entry stored in dbm for [ENSG00000234984.1] WARNING, no entry stored in dbm for [ENSG00000263278.2] WARNING, no entry stored in dbm for [ENSG00000257550.2] WARNING, no entry stored in dbm for [ENSG00000259660.2] WARNING, no entry stored in dbm for [ENSG00000255470.1] WARNING, no entry stored in dbm for [ENSG00000254275.6] WARNING, no entry stored in dbm for [ENSG00000223750.1] WARNING, no entry stored in dbm for [ENSG00000281344.1] WARNING, no entry stored in dbm for [ENSG00000272321.1] WARNING, no entry stored in dbm for [ENSG00000233937.7] WARNING, no entry stored in dbm for [ENSG00000187172.15] WARNING, no entry stored in dbm for [ENSG00000233937.7] WARNING, no entry stored in dbm for [ENSG00000248103.1] WARNING, no entry stored in dbm for [ENSG00000259295.6] WARNING, no entry stored in dbm for [ENSG00000270533.2] WARNING, no entry stored in dbm for [ENSG00000230223.8] WARNING, no entry stored in dbm for [ENSG00000227588.2] WARNING, no entry stored in dbm for [ENSG00000223490.2] WARNING, no entry stored in dbm for [ENSG00000236021.2] WARNING, no entry stored in dbm for [ENSG00000235904.3] WARNING, no entry stored in dbm for [ENSG00000236778.8] WARNING, no entry stored in dbm for [ENSG00000266405.3] WARNING, no entry stored in dbm for [ENSG00000233033.1] WARNING, no entry stored in dbm for [ENSG00000280273.2] WARNING, no entry stored in dbm for [ENSG00000240137.6] WARNING, no entry stored in dbm for [ENSG00000236800.1] WARNING, no entry stored in dbm for [ENSG00000268635.2] WARNING, no entry stored in dbm for [ENSG00000279733.1] WARNING, no entry stored in dbm for [ENSG00000280143.1] WARNING, no entry stored in dbm for [ENSG00000286720.1] WARNING, no entry stored in dbm for [ENSG00000239556.4] WARNING, no entry stored in dbm for [ENSG00000273192.1] WARNING, no entry stored in dbm for [ENSG00000273192.1] WARNING, no entry stored in dbm for [ENSG00000239665.8] WARNING, no entry stored in dbm for [ENSG00000231630.1] WARNING, no entry stored in dbm for [ENSG00000229021.2] WARNING, no entry stored in dbm for [ENSG00000225096.3] WARNING, no entry stored in dbm for [ENSG00000225096.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000232499.2] WARNING, no entry stored in dbm for [ENSG00000285812.1] WARNING, no entry stored in dbm for [ENSG00000286610.1] WARNING, no entry stored in dbm for [ENSG00000286782.1] WARNING, no entry stored in dbm for [ENSG00000259994.1] WARNING, no entry stored in dbm for [ENSG00000230628.1] WARNING, no entry stored in dbm for [ENSG00000230537.2] WARNING, no entry stored in dbm for [ENSG00000272078.1] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000232098.3] 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 [ENSG00000227220.1] WARNING, no entry stored in dbm for [ENSG00000236166.1] WARNING, no entry stored in dbm for [ENSG00000276805.2] WARNING, no entry stored in dbm for [ENSG00000233332.1] WARNING, no entry stored in dbm for [ENSG00000231113.2] WARNING, no entry stored in dbm for [ENSG00000204929.13] WARNING, no entry stored in dbm for [ENSG00000280734.3] WARNING, no entry stored in dbm for [ENSG00000253853.3] WARNING, no entry stored in dbm for [ENSG00000254319.6] WARNING, no entry stored in dbm for [ENSG00000277526.5] WARNING, no entry stored in dbm for [ENSG00000223804.5] WARNING, no entry stored in dbm for [ENSG00000263590.2] WARNING, no entry stored in dbm for [ENSG00000287374.1] WARNING, no entry stored in dbm for [ENSG00000227733.10] WARNING, no entry stored in dbm for [ENSG00000277125.1] WARNING, no entry stored in dbm for [ENSG00000166104.15] WARNING, no entry stored in dbm for [ENSG00000241991.1] WARNING, no entry stored in dbm for [ENSG00000230837.1] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000254497.1] WARNING, no entry stored in dbm for [ENSG00000249056.1] WARNING, no entry stored in dbm for [ENSG00000250910.8] WARNING, no entry stored in dbm for [ENSG00000251411.1] WARNING, no entry stored in dbm for [ENSG00000255468.7] WARNING, no entry stored in dbm for [ENSG00000284687.1] WARNING, no entry stored in dbm for [ENSG00000287860.1] WARNING, no entry stored in dbm for [ENSG00000270978.1] WARNING, no entry stored in dbm for [ENSG00000254102.2] WARNING, no entry stored in dbm for [ENSG00000280828.1] WARNING, no entry stored in dbm for [ENSG00000259275.4] WARNING, no entry stored in dbm for [ENSG00000232633.4] WARNING, no entry stored in dbm for [ENSG00000259605.3] WARNING, no entry stored in dbm for [ENSG00000253377.2] WARNING, no entry stored in dbm for [ENSG00000287576.1] WARNING, no entry stored in dbm for [ENSG00000222826.1] WARNING, no entry stored in dbm for [ENSG00000261054.1] WARNING, no entry stored in dbm for [ENSG00000244313.3] WARNING, no entry stored in dbm for [ENSG00000248898.3] WARNING, no entry stored in dbm for [ENSG00000228351.3] WARNING, no entry stored in dbm for [ENSG00000257094.1] WARNING, no entry stored in dbm for [ENSG00000258134.1] WARNING, no entry stored in dbm for [ENSG00000269032.1] WARNING, no entry stored in dbm for [ENSG00000233084.2] WARNING, no entry stored in dbm for [ENSG00000267605.7] WARNING, no entry stored in dbm for [ENSG00000267605.7] WARNING, no entry stored in dbm for [ENSG00000268543.1] WARNING, no entry stored in dbm for [ENSG00000232098.3] WARNING, no entry stored in dbm for [ENSG00000286201.1] WARNING, no entry stored in dbm for [ENSG00000274282.1] WARNING, no entry stored in dbm for [ENSG00000226063.1] WARNING, no entry stored in dbm for [ENSG00000286797.1] WARNING, no entry stored in dbm for [ENSG00000259106.1] WARNING, no entry stored in dbm for [ENSG00000284052.1] WARNING, no entry stored in dbm for [ENSG00000263159.1] WARNING, no entry stored in dbm for [ENSG00000268205.1] WARNING, no entry stored in dbm for [ENSG00000241529.3] WARNING, no entry stored in dbm for [ENSG00000268205.1] WARNING, no entry stored in dbm for [ENSG00000239899.3] WARNING, no entry stored in dbm for [ENSG00000282943.1] WARNING, no entry stored in dbm for [ENSG00000280054.1] WARNING, no entry stored in dbm for [ENSG00000241764.4] WARNING, no entry stored in dbm for [ENSG00000267328.1] WARNING, no entry stored in dbm for [ENSG00000239791.2] * STAR-Fusion complete. See output: /tmp/nxf.lT9KTs8yqN/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)