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/c4/4ea852999b4ab3ffb3bc56c268cbf6/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/4ea852999b4ab3ffb3bc56c268cbf6/.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.7vqfVkT7iS/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.7vqfVkT7iS/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.7vqfVkT7iS/./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.7vqfVkT7iS/ctat_genome_lib_build_dir -J /tmp/nxf.7vqfVkT7iS/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Chimeric.out.junction -O /tmp/nxf.7vqfVkT7iS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.7vqfVkT7iS/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Chimeric.out.junction -building interval tree based on /tmp/nxf.7vqfVkT7iS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=35294.12/min [20000], rate=37500.00/min [30000], rate=31034.48/min [40000], rate=27906.98/min [50000], rate=27272.73/min [60000], rate=28346.46/min [70000], rate=29166.67/min [80000], rate=30967.74/min [90000], rate=32530.12/min [100000], rate=31578.95/min [110000], rate=31730.77/min [120000], rate=32287.00/min [130000], rate=33191.49/min [140000], rate=33870.97/min [150000], rate=33582.09/min [160000], rate=33802.82/min [170000], rate=34693.88/min [180000], rate=36363.64/min [190000], rate=38000.00/min [200000], rate=38834.95/min [210000], rate=39622.64/min [220000], rate=40243.90/min [230000], rate=40469.21/min [240000], rate=40793.20/min [250000], rate=41095.89/min [260000], rate=41600.00/min [270000], rate=42297.65/min [280000], rate=42966.75/min [290000], rate=43500.00/min [300000], rate=42959.43/min [310000], rate=42465.75/min [320000], rate=42197.80/min [330000], rate=42307.69/min [340000], rate=41717.79/min [350000], rate=42253.52/min [360000], rate=42603.55/min [370000], rate=43106.80/min [380000], rate=43346.01/min [390000], rate=43656.72/min [400000], rate=44036.70/min [410000], rate=44324.32/min [420000], rate=44601.77/min [430000], rate=44947.74/min [440000], rate=45128.21/min [450000], rate=45075.13/min [460000], rate=45771.14/min [470000], rate=46611.57/min [480000], rate=47524.75/min [490000], rate=48355.26/min [500000], rate=49342.11/min [510000], rate=50246.31/min [520000], rate=51147.54/min [530000], rate=52045.83/min [540000], rate=52597.40/min [550000], rate=52969.50/min [560000], rate=53846.15/min [570000], rate=54028.44/min [580000], rate=54121.31/min [590000], rate=54461.54/min [600000], rate=54878.05/min [610000], rate=54062.04/min [620000], rate=54227.41/min [630000], rate=54545.45/min [640000], rate=54935.62/min [650000], rate=54852.32/min [660000], rate=54696.13/min [670000], rate=55144.03/min [680000], rate=55661.66/min [690000], rate=56403.27/min [700000], rate=56756.76/min [710000], rate=56875.83/min [720000], rate=56544.50/min [730000], rate=56081.95/min [740000], rate=54747.23/min [750000], rate=54086.54/min [760000], rate=54092.53/min [770000], rate=53596.29/min [780000], rate=53485.71/min [790000], rate=53079.51/min [800000], rate=52980.13/min [810000], rate=53231.11/min [820000], rate=52008.46/min [830000], rate=52037.62/min [840000], rate=51692.31/min [850000], rate=51204.82/min [860000], rate=51394.42/min [870000], rate=51888.67/min [880000], rate=52173.91/min [890000], rate=52662.72/min [900000], rate=53201.97/min [910000], rate=53687.32/min [920000], rate=54117.65/min [930000], rate=54174.76/min [940000], rate=53868.19/min [950000], rate=54234.06/min [960000], rate=54442.34/min [970000], rate=54341.74/min [980000], rate=54494.90/min [990000], rate=54847.65/min [1000000], rate=53763.44/min [1010000], rate=53580.90/min [1020000], rate=53684.21/min [1030000], rate=53599.31/min [1040000], rate=53151.62/min [1050000], rate=53030.30/min [1060000], rate=52736.32/min [1070000], rate=52839.51/min [1080000], rate=53027.82/min [1090000], rate=53431.37/min [1100000], rate=53745.93/min [1110000], rate=54190.40/min [1120000], rate=54634.15/min [1130000], rate=55032.47/min [1140000], rate=55384.62/min [1150000], rate=55690.07/min [1160000], rate=56129.03/min [1170000], rate=56476.27/min [1180000], rate=56867.47/min [1190000], rate=56847.13/min [1200000], rate=56559.31/min [1210000], rate=56410.26/min [1220000], rate=55750.19/min [1230000], rate=54910.71/min [1240000], rate=54705.88/min [1250000], rate=54426.71/min [1260000], rate=54506.13/min [1270000], rate=54506.44/min [1280000], rate=54275.62/min [1290000], rate=54315.79/min [1300000], rate=54129.08/min [1310000], rate=53651.88/min [1320000], rate=52905.81/min [1330000], rate=52088.77/min [1340000], rate=52275.68/min [1350000], rate=52495.14/min [1360000], rate=52543.46/min [1370000], rate=52759.95/min [1380000], rate=52705.28/min [1390000], rate=52851.71/min [1400000], rate=52664.58/min [1410000], rate=52875.00/min [1420000], rate=53117.21/min [1430000], rate=53457.94/min [1440000], rate=53598.01/min [1450000], rate=53703.70/min [1460000], rate=53742.33/min [1470000], rate=53714.98/min [1480000], rate=53688.03/min [1490000], rate=53629.27/min [1500000], rate=53667.26/min [1510000], rate=53672.99/min [1520000], rate=53615.52/min [1530000], rate=53403.14/min [1540000], rate=53225.81/min [1550000], rate=53051.91/min [1560000], rate=52911.25/min [1570000], rate=52951.10/min [1580000], rate=52813.37/min [1590000], rate=52794.69/min [1600000], rate=52718.29/min [1610000], rate=52614.38/min [1620000], rate=52568.96/min [1630000], rate=52637.24/min [1640000], rate=52648.48/min [1650000], rate=52132.70/min [1660000], rate=51606.22/min [1670000], rate=51253.20/min [1680000], rate=50883.39/min [1690000], rate=50598.80/min [1700000], rate=50271.07/min [1710000], rate=50171.15/min [1720000], rate=49663.14/min [1730000], rate=49217.64/min [1740000], rate=48853.53/min [1750000], rate=48611.11/min [1760000], rate=48507.12/min [1770000], rate=48493.15/min [1780000], rate=48457.35/min [1790000], rate=48356.60/min [1800000], rate=48322.15/min [1810000], rate=48159.65/min [1820000], rate=48042.23/min [1830000], rate=47989.51/min [1840000], rate=47916.67/min [1850000], rate=47927.46/min [1860000], rate=47917.56/min [1870000], rate=47989.73/min [1880000], rate=48163.96/min [1890000], rate=48214.29/min [1900000], rate=47939.44/min [1910000], rate=47710.24/min [1920000], rate=47290.64/min [1930000], rate=46844.66/min [1940000], rate=46597.28/min [1950000], rate=46391.75/min [1960000], rate=46262.79/min [1970000], rate=46207.97/min [1980000], rate=46082.23/min [1990000], rate=45887.78/min [2000000], rate=45801.53/min [2010000], rate=45647.24/min [2020000], rate=45563.91/min [2030000], rate=45635.07/min [2040000], rate=45705.75/min [2050000], rate=45741.91/min [2060000], rate=45726.97/min [2070000], rate=45712.18/min [2080000], rate=45497.63/min [2090000], rate=45189.19/min [2100000], rate=44951.84/min [2110000], rate=44624.60/min [2120000], rate=44228.09/min [2130000], rate=43977.98/min -building interval tree based on /tmp/nxf.7vqfVkT7iS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=24000.00/min [20000], rate=23076.92/min [30000], rate=26865.67/min [40000], rate=27586.21/min [50000], rate=27777.78/min [60000], rate=28800.00/min [70000], rate=29577.46/min [80000], rate=30967.74/min [90000], rate=32142.86/min [100000], rate=32608.70/min [110000], rate=34196.89/min [120000], rate=35467.98/min [130000], rate=36619.72/min [140000], rate=37668.16/min [150000], rate=39823.01/min [160000], rate=40000.00/min [170000], rate=38202.25/min [180000], rate=36860.07/min [190000], rate=34862.39/min [200000], rate=33707.87/min [210000], rate=33421.75/min [220000], rate=32195.12/min [230000], rate=31363.64/min [240000], rate=30062.63/min [250000], rate=29821.07/min [260000], rate=29770.99/min [270000], rate=30055.66/min [280000], rate=30324.91/min [290000], rate=30419.58/min [300000], rate=30664.40/min [310000], rate=31000.00/min [320000], rate=31321.37/min [330000], rate=31680.00/min [340000], rate=31875.00/min [350000], rate=32307.69/min [360000], rate=33078.10/min [370000], rate=33738.60/min [380000], rate=34285.71/min [390000], rate=34513.27/min [400000], rate=34682.08/min [410000], rate=35042.74/min [420000], rate=35443.04/min [430000], rate=35883.17/min [440000], rate=35918.37/min [450000], rate=35386.63/min [460000], rate=34629.86/min [470000], rate=33812.95/min [480000], rate=33410.67/min [490000], rate=33638.44/min [500000], rate=33296.34/min [510000], rate=33188.72/min [520000], rate=33050.85/min [530000], rate=33194.15/min [540000], rate=33128.83/min [550000], rate=33099.30/min [560000], rate=32812.50/min [570000], rate=32853.03/min [580000], rate=32676.06/min [590000], rate=32626.73/min [600000], rate=32549.73/min [610000], rate=32133.45/min [620000], rate=31876.61/min [630000], rate=32088.29/min [640000], rate=32080.20/min [650000], rate=32098.77/min [660000], rate=32352.94/min [670000], rate=32603.41/min [680000], rate=32929.78/min [690000], rate=33040.70/min [700000], rate=33227.85/min [710000], rate=33437.99/min [720000], rate=33618.68/min [730000], rate=33796.30/min [740000], rate=33815.69/min [750000], rate=34039.33/min [760000], rate=34080.72/min [770000], rate=34247.59/min [780000], rate=34411.76/min [790000], rate=34347.83/min [800000], rate=34408.60/min [810000], rate=34517.05/min [820000], rate=34794.91/min [830000], rate=34776.54/min [840000], rate=34686.85/min [850000], rate=34812.29/min [860000], rate=34935.68/min [870000], rate=35010.06/min [880000], rate=34943.75/min [890000], rate=35062.38/min [900000], rate=35156.25/min [910000], rate=35271.32/min [920000], rate=35498.39/min [930000], rate=35654.95/min [940000], rate=35764.11/min [950000], rate=35849.06/min [960000], rate=35820.90/min [970000], rate=36037.15/min [980000], rate=36073.62/min [990000], rate=36219.51/min [1000000], rate=36407.77/min [1010000], rate=36484.05/min [1020000], rate=36559.14/min [1030000], rate=36633.08/min [1040000], rate=36770.77/min [1050000], rate=36842.11/min [1060000], rate=36848.20/min [1070000], rate=36939.01/min [1080000], rate=37092.16/min [1090000], rate=37053.82/min [1100000], rate=37183.10/min [1110000], rate=37290.03/min [1120000], rate=37395.66/min [1130000], rate=37562.33/min [1140000], rate=37727.52/min [1150000], rate=37870.47/min [1160000], rate=37970.54/min [1170000], rate=38131.45/min [1180000], rate=38187.70/min [1190000], rate=38263.67/min [1200000], rate=38359.08/min [1210000], rate=38392.38/min [1220000], rate=38425.20/min [1230000], rate=38497.65/min [1240000], rate=38569.21/min [1250000], rate=38619.98/min [1260000], rate=38789.12/min [1270000], rate=38917.26/min [1280000], rate=39083.97/min [1290000], rate=39170.04/min [1300000], rate=39334.34/min [1310000], rate=39398.50/min [1320000], rate=39324.73/min [1330000], rate=39271.65/min [1340000], rate=39276.99/min [1350000], rate=39225.18/min [1360000], rate=39211.92/min [1370000], rate=39236.28/min [1380000], rate=39278.94/min [1390000], rate=39302.54/min [1400000], rate=39344.26/min [1410000], rate=39458.96/min [1420000], rate=39517.63/min [1430000], rate=39630.48/min [1440000], rate=39633.03/min [1450000], rate=39762.34/min [1460000], rate=39782.02/min [1470000], rate=39873.42/min [1480000], rate=40000.00/min [1490000], rate=40017.91/min [1500000], rate=40089.09/min [1510000], rate=40177.38/min [1520000], rate=40123.19/min [1530000], rate=40139.92/min [1540000], rate=40121.58/min [1550000], rate=40120.79/min [1560000], rate=40051.35/min [1570000], rate=39915.25/min [1580000], rate=39865.43/min [1590000], rate=39799.75/min [1600000], rate=39669.42/min [1610000], rate=39687.76/min [1620000], rate=39738.35/min [1630000], rate=39691.56/min [1640000], rate=39565.74/min [1650000], rate=39536.74/min [1660000], rate=39570.92/min [1670000], rate=39557.84/min [1680000], rate=39529.41/min [1690000], rate=39547.58/min [1700000], rate=39580.91/min [1710000], rate=39507.12/min [1720000], rate=39661.80/min [1730000], rate=39877.06/min [1740000], rate=40107.57/min [1750000], rate=40322.58/min [1760000], rate=40521.87/min [1770000], rate=40720.86/min [1780000], rate=40935.22/min [1790000], rate=41055.05/min [1800000], rate=41064.64/min [1810000], rate=41027.58/min [1820000], rate=40852.97/min [1830000], rate=40848.21/min [1840000], rate=40934.37/min [1850000], rate=40868.92/min [1860000], rate=40819.31/min [1870000], rate=40844.56/min [1880000], rate=40780.91/min [1890000], rate=40968.21/min [1900000], rate=41140.38/min [1910000], rate=41178.58/min [1920000], rate=41113.49/min [1930000], rate=40889.83/min [1940000], rate=40799.16/min [1950000], rate=40723.98/min [1960000], rate=40649.84/min [1970000], rate=40660.47/min [1980000], rate=40698.87/min [1990000], rate=40792.62/min [2000000], rate=40858.02/min [2010000], rate=40992.52/min [2020000], rate=41140.53/min [2030000], rate=41316.15/min [2040000], rate=41449.37/min [2050000], rate=41540.02/min [2060000], rate=41560.19/min [2070000], rate=41621.98/min [2080000], rate=41461.79/min [2090000], rate=41345.20/min [2100000], rate=41392.90/min [2110000], rate=41481.00/min -building interval tree based on /tmp/nxf.7vqfVkT7iS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=70588.24/min [30000], rate=69230.77/min [40000], rate=68571.43/min [50000], rate=78947.37/min [60000], rate=81818.18/min [70000], rate=93333.33/min [80000], rate=94117.65/min [90000], rate=81818.18/min [100000], rate=75949.37/min [110000], rate=71739.13/min [120000], rate=62068.97/min [130000], rate=58208.96/min [140000], rate=52500.00/min [150000], rate=54878.05/min [160000], rate=55813.95/min [170000], rate=55737.70/min [180000], rate=57754.01/min [190000], rate=57000.00/min [200000], rate=56603.77/min [210000], rate=55752.21/min [220000], rate=57641.92/min [230000], rate=59740.26/min [240000], rate=62068.97/min [250000], rate=64377.68/min [260000], rate=66952.79/min [270000], rate=69527.90/min [280000], rate=71794.87/min [290000], rate=74358.97/min [300000], rate=76595.74/min [310000], rate=78813.56/min [320000], rate=81012.66/min [330000], rate=82157.68/min [340000], rate=82926.83/min [350000], rate=81712.06/min [360000], rate=81203.01/min [370000], rate=79856.12/min [380000], rate=77551.02/min [390000], rate=77740.86/min [400000], rate=75709.78/min [410000], rate=76397.52/min [420000], rate=76132.93/min [430000], rate=74782.61/min [440000], rate=73333.33/min [450000], rate=72580.65/min [460000], rate=71875.00/min [470000], rate=70854.27/min [480000], rate=71111.11/min [490000], rate=72592.59/min [500000], rate=72463.77/min [510000], rate=73031.03/min [520000], rate=72558.14/min [530000], rate=72437.36/min [540000], rate=72645.74/min [550000], rate=73496.66/min [560000], rate=74336.28/min [570000], rate=75496.69/min [580000], rate=76651.98/min [590000], rate=77973.57/min [600000], rate=79295.15/min [610000], rate=80439.56/min [620000], rate=81758.24/min [630000], rate=82713.35/min [640000], rate=84026.26/min [650000], rate=85152.84/min [660000], rate=86274.51/min [670000], rate=85897.44/min [680000], rate=85894.74/min [690000], rate=85537.19/min [700000], rate=85539.71/min [710000], rate=84189.72/min [720000], rate=83397.68/min [730000], rate=82797.73/min [740000], rate=82990.65/min [750000], rate=83179.30/min [760000], rate=82758.62/min [770000], rate=83393.50/min [780000], rate=83720.93/min [790000], rate=84042.55/min [800000], rate=83333.33/min [810000], rate=82793.87/min [820000], rate=82550.34/min [830000], rate=83000.00/min [840000], rate=82894.74/min [850000], rate=83606.56/min [860000], rate=83630.47/min [870000], rate=83922.83/min [880000], rate=83942.77/min [890000], rate=84227.13/min [900000], rate=84905.66/min [910000], rate=85579.94/min [920000], rate=86115.44/min [930000], rate=86244.20/min [940000], rate=85844.75/min [950000], rate=85585.59/min [960000], rate=84830.63/min 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rate=47956.07/min [1320000], rate=46975.09/min [1330000], rate=46100.52/min [1340000], rate=45449.41/min [1350000], rate=44900.22/min [1360000], rate=44468.66/min [1370000], rate=44146.08/min [1380000], rate=43879.17/min [1390000], rate=43573.67/min [1400000], rate=43343.65/min [1410000], rate=43207.35/min [1420000], rate=43052.05/min [1430000], rate=42900.00/min [1440000], rate=42708.85/min [1450000], rate=42626.16/min [1460000], rate=42462.43/min [1470000], rate=42241.38/min [1480000], rate=42085.31/min [1490000], rate=41952.14/min [1500000], rate=41938.49/min [1510000], rate=41925.03/min [1520000], rate=41950.32/min [1530000], rate=41917.81/min [1540000], rate=41866.79/min [1550000], rate=41910.77/min [1560000], rate=41991.92/min [1570000], rate=42053.57/min [1580000], rate=42039.91/min [1590000], rate=42137.81/min [1600000], rate=42086.80/min [1610000], rate=41981.75/min [1620000], rate=41896.55/min [1630000], rate=41652.47/min [1640000], rate=41554.05/min [1650000], 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