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/7c/54af34423d30bb4eeea79b217f24b2/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/76a08aedc0c50212a3a43833a66967/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/b6414bfd0e4b2e793a78697e285566/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/76a08aedc0c50212a3a43833a66967/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/b6414bfd0e4b2e793a78697e285566/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.tVAeRScHj3/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.tVAeRScHj3/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.tVAeRScHj3/./star-fusion.preliminary -sample contains 219941146 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.tVAeRScHj3/ctat_genome_lib_build_dir -J /tmp/nxf.tVAeRScHj3/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.Chimeric.out.junction -O /tmp/nxf.tVAeRScHj3/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.tVAeRScHj3/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.tVAeRScHj3/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=23076.92/min [20000], rate=25531.91/min [30000], rate=27692.31/min [40000], rate=26666.67/min [50000], rate=24793.39/min [60000], rate=23376.62/min [70000], rate=22459.89/min [80000], rate=21621.62/min [90000], rate=21774.19/min [100000], rate=21660.65/min [110000], rate=21359.22/min [120000], rate=20689.66/min [130000], rate=21253.41/min [140000], rate=21374.05/min [150000], rate=21739.13/min [160000], rate=21768.71/min [170000], rate=22319.47/min [180000], rate=22784.81/min [190000], rate=23217.92/min [200000], rate=23809.52/min [210000], rate=24324.32/min [220000], rate=24719.10/min [230000], rate=25274.73/min [240000], rate=25352.11/min [250000], rate=25817.56/min [260000], rate=26351.35/min [270000], rate=26955.07/min [280000], rate=27406.20/min [290000], rate=27795.53/min [300000], rate=28257.46/min [310000], rate=27886.06/min [320000], rate=27467.81/min [330000], rate=27160.49/min [340000], rate=26877.47/min [350000], rate=26854.22/min [360000], rate=27376.43/min [370000], rate=27854.45/min [380000], rate=28322.98/min [390000], rate=28924.60/min [400000], rate=29339.85/min [410000], rate=29250.89/min [420000], rate=29234.34/min [430000], rate=29251.70/min [440000], rate=29333.33/min [450000], rate=29411.76/min [460000], rate=29455.71/min [470000], rate=29528.80/min [480000], rate=29690.72/min [490000], rate=29637.10/min [500000], rate=29673.59/min [510000], rate=29795.52/min [520000], rate=29885.06/min [530000], rate=30028.33/min [540000], rate=30167.60/min [550000], rate=30164.53/min [560000], rate=30107.53/min [570000], rate=30000.00/min [580000], rate=30077.79/min [590000], rate=30127.66/min [600000], rate=30328.56/min [610000], rate=30500.00/min [620000], rate=30718.41/min [630000], rate=30907.60/min [640000], rate=31042.85/min [650000], rate=31200.00/min [660000], rate=31353.92/min [670000], rate=31308.41/min [680000], rate=31384.62/min [690000], rate=31482.89/min [700000], rate=31602.71/min [710000], rate=31814.79/min [720000], rate=32023.72/min [730000], rate=31994.16/min [740000], rate=31805.16/min [750000], rate=31645.57/min [760000], rate=31535.27/min [770000], rate=31514.32/min [780000], rate=31815.09/min [790000], rate=32048.68/min [800000], rate=32279.76/min [810000], rate=32508.36/min [820000], rate=32647.64/min [830000], rate=32677.17/min [840000], rate=32876.71/min [850000], rate=33116.88/min [860000], rate=33333.33/min [870000], rate=33354.63/min [880000], rate=33249.37/min [890000], rate=33085.50/min [900000], rate=32747.12/min [910000], rate=32365.15/min [920000], rate=32130.38/min [930000], rate=31885.71/min [940000], rate=31667.60/min [950000], rate=31456.95/min [960000], rate=31253.39/min [970000], rate=31324.00/min [980000], rate=31477.52/min [990000], rate=31663.11/min [1000000], rate=31830.24/min [1010000], rate=32012.68/min [1020000], rate=32125.98/min [1030000], rate=31954.50/min [1040000], rate=32082.26/min [1050000], rate=32291.13/min [1060000], rate=32515.34/min [1070000], rate=32805.31/min [1080000], rate=33010.70/min [1090000], rate=33197.97/min [1100000], rate=33417.72/min [1110000], rate=33636.36/min [1120000], rate=33836.86/min [1130000], rate=34070.35/min [1140000], rate=34251.38/min [1150000], rate=34448.33/min [1160000], rate=34626.87/min [1170000], rate=34821.43/min [1180000], rate=35014.84/min [1190000], rate=35189.75/min [1200000], rate=35433.07/min [1210000], rate=35693.22/min [1220000], rate=35882.35/min [1230000], rate=36052.76/min [1240000], rate=36257.31/min [1250000], rate=36443.15/min [1260000], rate=36645.66/min [1270000], rate=36829.39/min [1280000], rate=37083.53/min [1290000], rate=37265.29/min [1300000], rate=37410.07/min [1310000], rate=37589.67/min [1320000], rate=37768.24/min [1330000], rate=37909.74/min [1340000], rate=38104.27/min [1350000], rate=38261.69/min [1360000], rate=38454.29/min [1370000], rate=38627.82/min [1380000], rate=38818.57/min [1390000], rate=39026.67/min [1400000], rate=39160.84/min [1410000], rate=39275.77/min [1420000], rate=39226.52/min [1430000], rate=39357.80/min [1440000], rate=39470.08/min [1450000], rate=39599.45/min [1460000], rate=39727.89/min [1470000], rate=39909.50/min [1480000], rate=40054.13/min [1490000], rate=40125.67/min [1500000], rate=40160.64/min [1510000], rate=40230.91/min [1520000], rate=40300.49/min [1530000], rate=40387.15/min [1540000], rate=40490.80/min [1550000], rate=40611.35/min [1560000], rate=40731.07/min [1570000], rate=40814.56/min [1580000], rate=40844.46/min [1590000], rate=40682.30/min [1600000], rate=40319.19/min [1610000], rate=40116.28/min [1620000], rate=39885.10/min [1630000], rate=39691.56/min [1640000], rate=39470.52/min [1650000], rate=39223.45/min [1660000], rate=38921.45/min [1670000], rate=38098.86/min [1680000], rate=37625.98/min [1690000], rate=37403.17/min [1700000], rate=37226.28/min [1710000], rate=37066.47/min [1720000], rate=36975.99/min [1730000], rate=37005.35/min [1740000], rate=36903.50/min [1750000], rate=36816.27/min [1760000], rate=36704.90/min [1770000], rate=36582.85/min [1780000], rate=36462.96/min [1790000], rate=36382.11/min [1800000], rate=36302.52/min [1810000], rate=36260.43/min [1820000], rate=36254.98/min [1830000], rate=36237.62/min [1840000], rate=36244.25/min [1850000], rate=36215.33/min [1860000], rate=36245.53/min [1870000], rate=36275.46/min [1880000], rate=36305.12/min [1890000], rate=36346.15/min [1900000], rate=36398.47/min [1910000], rate=36265.82/min [1920000], rate=36329.23/min [1930000], rate=36403.65/min [1940000], rate=36489.03/min [1950000], rate=36573.93/min [1960000], rate=36681.22/min [1970000], rate=36799.50/min -building interval tree based on /tmp/nxf.tVAeRScHj3/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=54545.45/min [30000], rate=46153.85/min [40000], rate=45283.02/min [50000], rate=43478.26/min [60000], rate=42857.14/min [70000], rate=42000.00/min [80000], rate=41025.64/min [90000], rate=40298.51/min [100000], rate=39735.10/min [110000], rate=37288.14/min [120000], rate=37894.74/min [130000], rate=38423.65/min [140000], rate=38888.89/min [150000], rate=40000.00/min [160000], rate=40851.06/min [170000], rate=41295.55/min [180000], rate=41538.46/min [190000], rate=41758.24/min [200000], rate=41811.85/min [210000], rate=42000.00/min [220000], rate=39879.15/min [230000], rate=37912.09/min [240000], rate=33802.82/min [250000], rate=30674.85/min [260000], rate=29942.42/min [270000], rate=30000.00/min [280000], rate=29893.24/min [290000], rate=29342.33/min [300000], rate=29411.76/min [310000], rate=29665.07/min [320000], rate=29860.03/min [330000], rate=30091.19/min [340000], rate=30312.04/min [350000], rate=30612.24/min [360000], rate=30857.14/min [370000], rate=31179.78/min [380000], rate=31448.28/min [390000], rate=31793.48/min [400000], rate=32128.51/min [410000], rate=32496.70/min [420000], rate=32898.17/min [430000], rate=33290.32/min [440000], rate=33502.54/min [450000], rate=33834.59/min [460000], rate=34158.42/min [470000], rate=34516.52/min [480000], rate=34866.83/min [490000], rate=35251.80/min [500000], rate=35587.19/min [510000], rate=35915.49/min [520000], rate=36236.93/min [530000], rate=36593.79/min [540000], rate=36944.13/min [550000], rate=37288.14/min [560000], rate=36801.75/min [570000], rate=36114.04/min [580000], rate=35987.59/min [590000], rate=35866.26/min [600000], rate=35785.29/min [610000], rate=36023.62/min [620000], rate=36081.47/min [630000], rate=36206.90/min [640000], rate=36260.62/min [650000], rate=36245.35/min [660000], rate=36263.74/min [670000], rate=36347.20/min [680000], rate=36428.57/min [690000], rate=36443.66/min [700000], rate=36426.71/min [710000], rate=36441.40/min [720000], rate=36517.33/min [730000], rate=36469.61/min [740000], rate=36543.21/min [750000], rate=36644.95/min [760000], rate=36744.56/min [770000], rate=36871.51/min [780000], rate=36996.05/min [790000], rate=37147.34/min [800000], rate=37325.04/min [810000], rate=37528.96/min [820000], rate=37701.15/min [830000], rate=37500.00/min [840000], rate=37333.33/min [850000], rate=37144.94/min [860000], rate=37015.78/min [870000], rate=37073.86/min [880000], rate=37288.14/min [890000], rate=37447.41/min [900000], rate=37011.65/min [910000], rate=36792.45/min [920000], rate=36196.72/min [930000], rate=35976.79/min [940000], rate=35877.86/min [950000], rate=35625.00/min [960000], rate=35555.56/min [970000], rate=35596.33/min [980000], rate=35614.78/min [990000], rate=35399.28/min [1000000], rate=35377.36/min [1010000], rate=35417.88/min [1020000], rate=35457.71/min [1030000], rate=35558.11/min [1040000], rate=35616.44/min [1050000], rate=35633.48/min [1060000], rate=35690.24/min [1070000], rate=35785.95/min [1080000], rate=35840.71/min [1090000], rate=35934.07/min [1100000], rate=36006.55/min [1110000], rate=36019.47/min [1120000], rate=36032.17/min [1130000], rate=36083.02/min [1140000], rate=36018.96/min [1150000], rate=36106.75/min [1160000], rate=36099.59/min [1170000], rate=36204.23/min [1180000], rate=36326.32/min [1190000], rate=36428.57/min [1200000], rate=36492.65/min [1210000], rate=36629.67/min [1220000], rate=36765.44/min [1230000], rate=36918.46/min [1240000], rate=36868.19/min [1250000], rate=36692.76/min [1260000], rate=36878.05/min [1270000], rate=37026.24/min [1280000], rate=37191.28/min [1290000], rate=37337.19/min [1300000], rate=37284.89/min [1310000], rate=36797.75/min [1320000], rate=36447.31/min [1330000], rate=36421.73/min [1340000], rate=36396.56/min [1350000], rate=36420.86/min [1360000], rate=36379.85/min [1370000], rate=36084.28/min [1380000], rate=36125.65/min [1390000], rate=36182.21/min [1400000], rate=36238.14/min [1410000], rate=36293.44/min [1420000], rate=35994.93/min [1430000], rate=35794.74/min [1440000], rate=35614.18/min [1450000], rate=35437.88/min [1460000], rate=35336.83/min [1470000], rate=35251.80/min [1480000], rate=35057.24/min [1490000], rate=34949.18/min [1500000], rate=34843.21/min [1510000], rate=34725.95/min [1520000], rate=34519.30/min [1530000], rate=34317.76/min [1540000], rate=34234.90/min [1550000], rate=34203.75/min [1560000], rate=34210.53/min [1570000], rate=34204.79/min [1580000], rate=34211.48/min [1590000], rate=34218.08/min [1600000], rate=34261.24/min [1610000], rate=34086.10/min [1620000], rate=33832.23/min [1630000], rate=33596.70/min [1640000], rate=33401.22/min [1650000], rate=33445.95/min [1660000], rate=33524.07/min [1670000], rate=33601.61/min [1680000], rate=33678.58/min [1690000], rate=33721.32/min [1700000], rate=33808.42/min [1710000], rate=33906.15/min [1720000], rate=34003.29/min [1730000], rate=34077.48/min [1740000], rate=34184.68/min [1750000], rate=34246.58/min [1760000], rate=34352.64/min [1770000], rate=34335.60/min [1780000], rate=34418.30/min [1790000], rate=34500.48/min [1800000], rate=34515.82/min [1810000], rate=34541.98/min [1820000], rate=34600.76/min [1830000], rate=34637.22/min [1840000], rate=34651.60/min [1850000], rate=34709.19/min [1860000], rate=34788.03/min [1870000], rate=34866.38/min [1880000], rate=34933.42/min [1890000], rate=35010.81/min [1900000], rate=35076.92/min [1910000], rate=35164.16/min [1920000], rate=35250.92/min [1930000], rate=35304.88/min [1940000], rate=35347.71/min [1950000], rate=35454.55/min [1960000], rate=35550.18/min [1970000], rate=35645.36/min -building interval tree based on /tmp/nxf.tVAeRScHj3/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=35294.12/min [20000], rate=40000.00/min [30000], rate=41860.47/min [40000], rate=44444.44/min [50000], rate=46153.85/min [60000], rate=46753.25/min [70000], rate=48837.21/min [80000], rate=48979.59/min [90000], rate=50467.29/min [100000], rate=50847.46/min [110000], rate=51562.50/min [120000], rate=51428.57/min [130000], rate=52000.00/min [140000], rate=51851.85/min [150000], rate=52325.58/min [160000], rate=52747.25/min [170000], rate=53684.21/min [180000], rate=55102.04/min [190000], rate=55609.76/min [200000], rate=56603.77/min [210000], rate=57013.57/min [220000], rate=56896.55/min [230000], rate=56790.12/min [240000], rate=54961.83/min [250000], rate=54151.62/min [260000], rate=54166.67/min [270000], rate=53642.38/min [280000], rate=53846.15/min [290000], rate=53048.78/min [300000], rate=52173.91/min [310000], rate=51239.67/min [320000], rate=50393.70/min [330000], rate=50000.00/min [340000], rate=48803.83/min [350000], rate=48723.90/min [360000], rate=48106.90/min [370000], rate=47639.48/min [380000], rate=47599.16/min [390000], rate=47755.10/min [400000], rate=47337.28/min [410000], rate=47490.35/min [420000], rate=47727.27/min [430000], rate=47252.75/min [440000], rate=46975.09/min [450000], rate=47368.42/min [460000], rate=47586.21/min [470000], rate=47796.61/min [480000], rate=47135.84/min [490000], rate=47115.38/min [500000], rate=45801.53/min [510000], rate=44028.78/min [520000], rate=42391.30/min [530000], rate=42287.23/min [540000], rate=40652.45/min [550000], rate=39426.52/min [560000], rate=38356.16/min [570000], rate=37500.00/min [580000], rate=37339.06/min [590000], rate=37579.62/min [600000], rate=37775.45/min [610000], rate=37966.80/min [620000], rate=38232.27/min [630000], rate=38414.63/min [640000], rate=38670.69/min [650000], rate=39039.04/min [660000], rate=39402.99/min [670000], rate=39723.32/min [680000], rate=40039.25/min [690000], rate=40116.28/min [700000], rate=39886.04/min [710000], rate=39738.81/min [720000], rate=39024.39/min [730000], rate=38864.24/min [740000], rate=38777.29/min [750000], rate=38659.79/min [760000], rate=38611.35/min [770000], rate=38628.76/min [780000], rate=38518.52/min [790000], rate=38041.73/min [800000], rate=37974.68/min [810000], rate=38057.95/min [820000], rate=37904.47/min [830000], rate=38015.27/min [840000], rate=37837.84/min [850000], rate=37582.90/min [860000], rate=37175.79/min [870000], rate=36812.41/min [880000], rate=36923.08/min [890000], rate=37006.24/min [900000], rate=37037.04/min [910000], rate=37142.86/min [920000], rate=37146.70/min [930000], rate=37175.22/min [940000], rate=36910.99/min [950000], rate=37037.04/min [960000], rate=37209.30/min [970000], rate=37188.50/min [980000], rate=36842.11/min [990000], rate=36175.40/min [1000000], rate=35928.14/min [1010000], rate=35689.05/min [1020000], rate=35253.46/min [1030000], rate=35173.59/min [1040000], rate=35214.45/min [1050000], rate=34864.42/min [1060000], rate=34322.72/min [1070000], rate=33950.29/min [1080000], rate=33732.43/min [1090000], rate=33780.99/min [1100000], rate=33898.31/min [1110000], rate=33996.94/min [1120000], rate=34111.68/min [1130000], rate=34259.73/min [1140000], rate=34371.86/min [1150000], rate=34294.23/min [1160000], rate=34370.37/min [1170000], rate=34513.27/min [1180000], rate=34654.92/min [1190000], rate=34761.44/min [1200000], rate=34833.09/min [1210000], rate=34903.85/min [1220000], rate=34642.69/min [1230000], rate=34615.38/min [1240000], rate=34604.65/min [1250000], rate=34706.15/min [1260000], rate=34822.66/min [1270000], rate=34858.19/min [1280000], rate=34641.41/min [1290000], rate=34476.61/min [1300000], rate=34589.80/min [1310000], rate=34701.99/min [1320000], rate=34859.15/min [1330000], rate=34892.87/min [1340000], rate=34625.32/min [1350000], rate=34292.97/min [1360000], rate=34042.55/min [1370000], rate=33855.02/min [1380000], rate=33400.56/min [1390000], rate=32860.52/min [1400000], rate=32282.86/min [1410000], rate=31780.62/min [1420000], rate=31289.02/min [1430000], rate=31154.68/min [1440000], rate=31123.92/min [1450000], rate=31093.64/min [1460000], rate=31085.88/min [1470000], rate=31089.18/min [1480000], rate=31103.33/min [1490000], rate=31117.30/min [1500000], rate=31131.10/min [1510000], rate=31166.15/min [1520000], rate=31200.82/min [1530000], rate=31224.49/min [1540000], rate=31258.46/min [1550000], rate=31334.23/min [1560000], rate=31419.94/min [1570000], rate=31483.96/min [1580000], rate=31318.14/min [1590000], rate=31034.48/min [1600000], rate=30818.62/min [1610000], rate=30627.77/min [1620000], rate=30460.67/min [1630000], rate=30297.40/min [1640000], rate=30045.80/min [1650000], rate=29846.25/min [1660000], rate=29616.41/min [1670000], rate=29384.16/min [1680000], rate=29336.44/min [1690000], rate=29382.79/min [1700000], rate=29437.23/min [1710000], rate=29264.12/min [1720000], rate=29119.64/min [1730000], rate=29140.93/min [1740000], rate=29227.32/min [1750000], rate=29321.42/min [1760000], rate=29415.04/min [1770000], rate=29516.40/min [1780000], rate=29609.09/min [1790000], rate=29701.33/min [1800000], rate=29801.32/min [1810000], rate=29900.88/min [1820000], rate=30008.24/min [1830000], rate=30106.94/min [1840000], rate=30213.46/min [1850000], rate=30319.58/min [1860000], rate=30425.30/min [1870000], rate=30497.42/min [1880000], rate=30593.98/min [1890000], rate=30681.82/min [1900000], rate=30760.93/min [1910000], rate=30856.22/min [1920000], rate=30942.79/min [1930000], rate=31045.58/min [1940000], rate=31139.65/min [1950000], rate=31067.45/min [1960000], rate=30906.70/min