Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/fe6be0afd233563a374fa5f66e9f3b/ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1_1.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/66/36817c11d86294b6f21a9400c73534/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/36817c11d86294b6f21a9400c73534/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/fe6be0afd233563a374fa5f66e9f3b/ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/79d41d845d919e12d76bc84f4807d2/ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.NMS43luF0E/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.NMS43luF0E/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.NMS43luF0E/./star-fusion.preliminary -sample contains 108305891 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.NMS43luF0E/ctat_genome_lib_build_dir -J /tmp/nxf.NMS43luF0E/ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.NMS43luF0E/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.NMS43luF0E/ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.NMS43luF0E/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=40000.00/min [20000], rate=46153.85/min [30000], rate=50000.00/min [40000], rate=51063.83/min [50000], rate=51724.14/min [60000], rate=48000.00/min [70000], rate=47727.27/min [80000], rate=48979.59/min [90000], rate=50943.40/min [100000], rate=53097.35/min [110000], rate=55462.18/min [120000], rate=56692.91/min [130000], rate=58646.62/min [140000], rate=60869.57/min [150000], rate=62500.00/min [160000], rate=60377.36/min [170000], rate=55737.70/min [180000], rate=54545.45/min [190000], rate=53521.13/min [200000], rate=53333.33/min [210000], rate=53617.02/min [220000], rate=53877.55/min [230000], rate=52272.73/min [240000], rate=52173.91/min [250000], rate=52264.81/min [260000], rate=52702.70/min [270000], rate=53289.47/min [280000], rate=52996.85/min [290000], rate=53211.01/min [300000], rate=53892.22/min [310000], rate=54545.45/min [320000], rate=55172.41/min [330000], rate=55774.65/min [340000], rate=56666.67/min [350000], rate=57377.05/min [360000], rate=58064.52/min [370000], rate=58885.94/min [380000], rate=59842.52/min [390000], rate=60779.22/min [400000], rate=60759.49/min [410000], rate=60740.74/min [420000], rate=60000.00/min [430000], rate=59038.90/min [440000], rate=59060.40/min [450000], rate=59080.96/min [460000], rate=58350.95/min [470000], rate=58144.33/min [480000], rate=58181.82/min [490000], rate=58217.82/min [500000], rate=58593.75/min [510000], rate=58846.15/min [520000], rate=58979.21/min [530000], rate=59217.88/min [540000], rate=59449.54/min [550000], rate=59674.50/min [560000], rate=60000.00/min [570000], rate=60317.46/min [580000], rate=60732.98/min [590000], rate=61351.82/min [600000], rate=61643.84/min [610000], rate=61512.61/min [620000], rate=61589.40/min [630000], rate=61865.79/min [640000], rate=62236.63/min [650000], rate=62801.93/min [660000], rate=63258.79/min [670000], rate=63009.40/min [680000], rate=62672.81/min [690000], rate=61698.96/min [700000], rate=61135.37/min [710000], rate=60597.44/min [720000], rate=60335.20/min [730000], rate=59836.07/min [740000], rate=59517.43/min [750000], rate=59602.65/min [760000], rate=59764.09/min [770000], rate=59459.46/min [780000], rate=59693.88/min [790000], rate=59324.16/min [800000], rate=59186.19/min [810000], rate=59196.10/min [820000], rate=58992.81/min [830000], rate=58934.91/min [840000], rate=58878.50/min [850000], rate=58959.54/min [860000], rate=59174.31/min [870000], rate=59318.18/min [880000], rate=59526.49/min [890000], rate=59598.21/min [900000], rate=59800.66/min [910000], rate=60066.01/min [920000], rate=60327.87/min [930000], rate=60586.32/min [940000], rate=60907.13/min [950000], rate=61158.80/min [960000], rate=61472.79/min [970000], rate=61717.92/min [980000], rate=61699.90/min [990000], rate=61618.26/min [1000000], rate=61601.64/min [1010000], rate=61585.37/min [1020000], rate=61507.54/min [1030000], rate=61492.54/min [1040000], rate=61599.21/min [1050000], rate=61704.21/min [1060000], rate=61867.70/min [1070000], rate=62088.97/min [1080000], rate=62247.84/min [1090000], rate=62464.18/min [1100000], rate=62618.60/min [1110000], rate=62889.52/min [1120000], rate=63098.59/min [1130000], rate=63423.76/min [1140000], rate=63805.97/min [1150000], rate=64305.68/min [1160000], rate=64684.01/min [1170000], rate=64939.87/min [1180000], rate=65013.77/min [1190000], rate=65027.32/min [1200000], rate=65099.46/min [1210000], rate=65170.56/min [1220000], rate=65240.64/min [1230000], rate=65367.58/min [1240000], rate=65492.96/min [1250000], rate=65616.80/min [1260000], rate=65739.13/min [1270000], rate=65859.98/min [1280000], rate=66092.94/min [1290000], rate=66267.12/min [1300000], rate=66439.52/min [1310000], rate=66610.17/min [1320000], rate=66779.09/min [1330000], rate=67058.82/min [1340000], rate=67280.33/min [1350000], rate=67669.17/min [1360000], rate=67943.38/min [1370000], rate=68159.20/min [1380000], rate=68429.75/min [1390000], rate=68641.98/min [1400000], rate=68965.52/min [1410000], rate=68948.66/min [1420000], rate=68932.04/min [1430000], rate=68971.06/min [1440000], rate=69009.58/min [1450000], rate=69102.46/min [1460000], rate=69139.70/min [1470000], rate=69285.15/min [1480000], rate=69429.24/min [1490000], rate=69571.98/min [1500000], rate=69767.44/min [1510000], rate=69799.69/min [1520000], rate=69938.65/min [1530000], rate=70129.87/min [1540000], rate=70266.16/min [1550000], rate=70507.96/min [1560000], rate=70801.82/min [1570000], rate=70987.19/min [1580000], rate=71171.17/min [1590000], rate=71353.78/min -building interval tree based on /tmp/nxf.NMS43luF0E/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=85714.29/min [30000], rate=78260.87/min [40000], rate=75000.00/min [50000], rate=81081.08/min [60000], rate=83720.93/min [70000], rate=80769.23/min [80000], rate=81355.93/min [90000], rate=76056.34/min [100000], rate=73170.73/min [110000], rate=73333.33/min [120000], rate=75789.47/min [130000], rate=77227.72/min [140000], rate=78504.67/min [150000], rate=78947.37/min [160000], rate=73846.15/min [170000], rate=68456.38/min [180000], rate=64670.66/min [190000], rate=62637.36/min [200000], rate=62827.23/min [210000], rate=62376.24/min [220000], rate=60829.49/min [230000], rate=59740.26/min [240000], rate=59751.04/min [250000], rate=60240.96/min [260000], rate=60700.39/min [270000], rate=61596.96/min [280000], rate=61992.62/min [290000], rate=62365.59/min [300000], rate=63604.24/min [310000], rate=65034.97/min [320000], rate=65979.38/min [330000], rate=67118.64/min [340000], rate=68227.42/min [350000], rate=69078.95/min [360000], rate=71052.63/min [370000], rate=72786.89/min [380000], rate=74025.97/min [390000], rate=75241.16/min [400000], rate=74534.16/min [410000], rate=74096.39/min [420000], rate=73469.39/min [430000], rate=73295.45/min [440000], rate=72727.27/min [450000], rate=72386.06/min [460000], rate=72062.66/min [470000], rate=72868.22/min [480000], rate=73657.29/min [490000], rate=73134.33/min [500000], rate=72289.16/min [510000], rate=72169.81/min [520000], rate=71889.40/min [530000], rate=71783.30/min [540000], rate=71523.18/min [550000], rate=71895.42/min [560000], rate=72413.79/min [570000], rate=73233.40/min [580000], rate=73885.35/min [590000], rate=74369.75/min [600000], rate=74534.16/min [610000], rate=74089.07/min [620000], rate=73228.35/min [630000], rate=71590.91/min [640000], rate=70848.71/min [650000], rate=69642.86/min [660000], rate=68393.78/min [670000], rate=67224.08/min [680000], rate=67105.26/min [690000], rate=66240.00/min [700000], rate=65727.70/min [710000], rate=65437.79/min [720000], rate=65553.87/min [730000], rate=65667.17/min [740000], rate=65680.47/min [750000], rate=65885.80/min [760000], rate=65611.51/min [770000], rate=65811.97/min [780000], rate=65822.78/min [790000], rate=66016.71/min [800000], rate=66024.76/min [810000], rate=65675.68/min [820000], rate=65425.53/min [830000], rate=65354.33/min [840000], rate=65284.97/min [850000], rate=65384.62/min [860000], rate=65565.44/min [870000], rate=65660.38/min [880000], rate=65265.76/min [890000], rate=65201.47/min [900000], rate=65454.55/min [910000], rate=65546.22/min [920000], rate=65636.15/min [930000], rate=65647.06/min [940000], rate=65505.23/min [950000], rate=65517.24/min [960000], rate=65454.55/min [970000], rate=65540.54/min [980000], rate=65698.32/min [990000], rate=65780.73/min [1000000], rate=65861.69/min [1010000], rate=66013.07/min [1020000], rate=66162.16/min [1030000], rate=66237.94/min [1040000], rate=66312.43/min [1050000], rate=66385.67/min [1060000], rate=66527.20/min [1070000], rate=66597.51/min [1080000], rate=66804.12/min [1090000], rate=67008.20/min [1100000], rate=67278.29/min [1110000], rate=67477.20/min [1120000], rate=67741.94/min [1130000], rate=68072.29/min [1140000], rate=68195.41/min [1150000], rate=67713.44/min [1160000], rate=67246.38/min [1170000], rate=66920.88/min [1180000], rate=66603.95/min [1190000], rate=66356.88/min [1200000], rate=66176.47/min [1210000], rate=66000.00/min [1220000], rate=65827.34/min [1230000], rate=65892.86/min [1240000], rate=65899.03/min [1250000], rate=65963.06/min [1260000], rate=66083.92/min [1270000], rate=66145.83/min [1280000], rate=66206.90/min [1290000], rate=66323.91/min [1300000], rate=66326.53/min [1310000], rate=66441.25/min [1320000], rate=66610.60/min [1330000], rate=66778.24/min [1340000], rate=66888.52/min [1350000], rate=66997.52/min [1360000], rate=67105.26/min [1370000], rate=67211.77/min [1380000], rate=67262.39/min [1390000], rate=67421.18/min [1400000], rate=67632.85/min [1410000], rate=67842.82/min [1420000], rate=68051.12/min [1430000], rate=68203.50/min [1440000], rate=68354.43/min [1450000], rate=68557.92/min [1460000], rate=68759.81/min [1470000], rate=68906.25/min [1480000], rate=69051.32/min [1490000], rate=69356.09/min [1500000], rate=69444.44/min [1510000], rate=69585.25/min [1520000], rate=69724.77/min [1530000], rate=69916.22/min [1540000], rate=70053.07/min [1550000], rate=70082.89/min [1560000], rate=70007.48/min [1570000], rate=69726.13/min [1580000], rate=69603.52/min -building interval tree based on /tmp/nxf.NMS43luF0E/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=16216.22/min [20000], rate=18181.82/min [30000], rate=20000.00/min [40000], rate=22222.22/min [50000], rate=23076.92/min [60000], rate=23376.62/min [70000], rate=24705.88/min [80000], rate=24742.27/min [90000], rate=25233.64/min [100000], rate=25210.08/min [110000], rate=26190.48/min [120000], rate=26470.59/min [130000], rate=26712.33/min [140000], rate=27814.57/min [150000], rate=28481.01/min [160000], rate=29357.80/min [170000], rate=30177.51/min [180000], rate=30857.14/min [190000], rate=31491.71/min [200000], rate=32520.33/min [210000], rate=33600.00/min [220000], rate=34645.67/min [230000], rate=35751.30/min [240000], rate=36828.64/min [250000], rate=37878.79/min [260000], rate=38329.24/min [270000], rate=38388.63/min [280000], rate=38009.05/min [290000], rate=37339.06/min [300000], rate=36960.99/min [310000], rate=36399.22/min [320000], rate=36711.28/min [330000], rate=36940.30/min [340000], rate=36756.76/min [350000], rate=36649.21/min [360000], rate=36548.22/min [370000], rate=36513.16/min [380000], rate=36893.20/min [390000], rate=37320.57/min [400000], rate=37795.28/min [410000], rate=37904.47/min [420000], rate=38009.05/min [430000], rate=38392.86/min [440000], rate=38709.68/min [450000], rate=39130.43/min [460000], rate=39484.98/min [470000], rate=39774.33/min [480000], rate=39779.01/min [490000], rate=40109.14/min [500000], rate=40268.46/min [510000], rate=40637.45/min [520000], rate=40998.69/min [530000], rate=41352.41/min [540000], rate=41698.84/min [550000], rate=41878.17/min [560000], rate=42105.26/min [570000], rate=42537.31/min [580000], rate=42962.96/min [590000], rate=43329.25/min [600000], rate=43795.62/min [610000], rate=44256.35/min [620000], rate=44765.34/min [630000], rate=45269.46/min [640000], rate=45659.93/min [650000], rate=45828.44/min [660000], rate=45886.44/min [670000], rate=46048.11/min [680000], rate=46311.01/min [690000], rate=46674.18/min [700000], rate=46875.00/min [710000], rate=47280.80/min [720000], rate=47629.55/min [730000], rate=48026.32/min [740000], rate=48471.62/min [750000], rate=48913.04/min [760000], rate=49244.06/min [770000], rate=49624.06/min [780000], rate=50053.48/min [790000], rate=50479.23/min [800000], rate=50847.46/min [810000], rate=51211.80/min [820000], rate=51410.66/min [830000], rate=51875.00/min [840000], rate=52282.16/min [850000], rate=52415.21/min [860000], rate=52545.82/min [870000], rate=52780.59/min [880000], rate=53172.21/min [890000], rate=53453.45/min [900000], rate=53784.86/min [910000], rate=54005.93/min [920000], rate=54223.97/min [930000], rate=54705.88/min [940000], rate=55024.39/min [950000], rate=55286.13/min [960000], rate=55598.46/min [970000], rate=55907.78/min [980000], rate=56321.84/min [990000], rate=56571.43/min [1000000], rate=56926.00/min [1010000], rate=57223.80/min [1020000], rate=57303.37/min [1030000], rate=57488.37/min [1040000], rate=57777.78/min [1050000], rate=58064.52/min [1060000], rate=58241.76/min [1070000], rate=58576.64/min [1080000], rate=58909.09/min [1090000], rate=59132.01/min [1100000], rate=59405.94/min [1110000], rate=59677.42/min [1120000], rate=59893.05/min [1130000], rate=60213.14/min [1140000], rate=60477.45/min [1150000], rate=60792.95/min [1160000], rate=61052.63/min [1170000], rate=61256.54/min [1180000], rate=61405.03/min [1190000], rate=61604.83/min [1200000], rate=61802.58/min [1210000], rate=62051.28/min [1220000], rate=62244.90/min [1230000], rate=62436.55/min [1240000], rate=62679.02/min [1250000], rate=62866.72/min [1260000], rate=63052.54/min [1270000], rate=63236.51/min [1280000], rate=63418.66/min [1290000], rate=63599.01/min [1300000], rate=63569.68/min [1310000], rate=63489.50/min [1320000], rate=63410.73/min [1330000], rate=63434.02/min [1340000], rate=63507.11/min [1350000], rate=63479.62/min [1360000], rate=63452.57/min [1370000], rate=63425.93/min [1380000], rate=63351.19/min [1390000], rate=63422.05/min [1400000], rate=63348.42/min [1410000], rate=63370.79/min [1420000], rate=63534.68/min [1430000], rate=63602.67/min [1440000], rate=63716.81/min [1450000], rate=63829.79/min [1460000], rate=63801.89/min [1470000], rate=63959.39/min [1480000], rate=64115.52/min [1490000], rate=64224.14/min [1500000], rate=64377.68/min [1510000], rate=64529.91/min [1520000], rate=64726.76/min [1530000], rate=64968.15/min [1540000], rate=65162.20/min [1550000], rate=65400.84/min [1560000], rate=65684.21/min [1570000], rate=65874.13/min [1580000], rate=65924.90/min [1590000], rate=65975.10/min