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/46/1f2e8948827d6364f3ed65a9cf09ba/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/38e039e8e18e618818086c0c2abc34/aih-tih-sc-446670-R1_B23WHYVLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/1f2e8948827d6364f3ed65a9cf09ba/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/38e039e8e18e618818086c0c2abc34/aih-tih-sc-446670-R1_B23WHYVLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/e95e58a1d4bce64d368d2c09cb7636/aih-tih-sc-446670-R1_B23WHYVLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.ZKvbNRKf7e/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.ZKvbNRKf7e/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.ZKvbNRKf7e/./star-fusion.preliminary -sample contains 222001508 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.ZKvbNRKf7e/ctat_genome_lib_build_dir -J /tmp/nxf.ZKvbNRKf7e/aih-tih-sc-446670-R1_B23WHYVLT4_1.Chimeric.out.junction -O /tmp/nxf.ZKvbNRKf7e/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.ZKvbNRKf7e/aih-tih-sc-446670-R1_B23WHYVLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.ZKvbNRKf7e/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=36363.64/min [30000], rate=36734.69/min [40000], rate=36363.64/min [50000], rate=37037.04/min [60000], rate=37113.40/min [70000], rate=37500.00/min [80000], rate=37500.00/min [90000], rate=39130.43/min [100000], rate=39473.68/min [110000], rate=39759.04/min [120000], rate=40449.44/min [130000], rate=40414.51/min [140000], rate=39622.64/min [150000], rate=39301.31/min [160000], rate=40000.00/min [170000], rate=40637.45/min [180000], rate=41379.31/min [190000], rate=41911.76/min [200000], rate=42553.19/min [210000], rate=43003.41/min [220000], rate=42443.73/min [230000], rate=42461.54/min [240000], rate=42985.07/min [250000], rate=43352.60/min [260000], rate=43454.04/min [270000], rate=44141.69/min [280000], rate=44680.85/min [290000], rate=44961.24/min [300000], rate=45454.55/min [310000], rate=46153.85/min [320000], rate=46601.94/min [330000], rate=47368.42/min [340000], rate=48226.95/min [350000], rate=48498.85/min [360000], rate=48000.00/min [370000], rate=48577.68/min [380000], rate=48717.95/min [390000], rate=47657.84/min [400000], rate=47058.82/min [410000], rate=46327.68/min [420000], rate=45818.18/min [430000], rate=45422.54/min [440000], rate=45051.19/min [450000], rate=44628.10/min [460000], rate=44230.77/min [470000], rate=43788.82/min [480000], rate=43504.53/min [490000], rate=43298.97/min [500000], rate=42857.14/min [510000], rate=42797.20/min [520000], rate=42798.35/min [530000], rate=42513.37/min [540000], rate=41485.28/min [550000], rate=40993.79/min [560000], rate=40975.61/min [570000], rate=41056.42/min [580000], rate=41086.19/min [590000], rate=41019.70/min [600000], rate=40449.44/min [610000], rate=40131.58/min [620000], rate=40216.22/min [630000], rate=40255.59/min [640000], rate=40378.55/min [650000], rate=40540.54/min [660000], rate=40615.38/min [670000], rate=40812.18/min [680000], rate=41005.03/min [690000], rate=41235.06/min [700000], rate=41501.98/min [710000], rate=41723.80/min [720000], rate=42023.35/min [730000], rate=42318.84/min [740000], rate=42569.51/min [750000], rate=42816.37/min [760000], rate=42379.18/min [770000], rate=42076.50/min [780000], rate=42352.94/min [790000], rate=42587.60/min [800000], rate=42818.91/min [810000], rate=43085.11/min [820000], rate=43348.02/min [830000], rate=43569.55/min [840000], rate=43826.09/min [850000], rate=44041.45/min [860000], rate=44215.94/min [870000], rate=44199.83/min [880000], rate=44295.30/min [890000], rate=44500.00/min [900000], rate=44701.99/min [910000], rate=44938.27/min [920000], rate=45134.91/min [930000], rate=45182.19/min [940000], rate=45264.85/min [950000], rate=45310.02/min [960000], rate=45390.07/min [970000], rate=45468.75/min [980000], rate=45581.40/min [990000], rate=45343.51/min [1000000], rate=45523.52/min [1010000], rate=45666.92/min [1020000], rate=45842.70/min [1030000], rate=46016.38/min [1040000], rate=46188.01/min [1050000], rate=46323.53/min [1060000], rate=46491.23/min [1070000], rate=46690.91/min [1080000], rate=46854.66/min [1090000], rate=47016.53/min [1100000], rate=47244.09/min [1110000], rate=47673.59/min [1120000], rate=47897.36/min [1130000], rate=48221.91/min [1140000], rate=48407.64/min [1150000], rate=48625.79/min [1160000], rate=48842.11/min [1170000], rate=48988.14/min [1180000], rate=49166.67/min [1190000], rate=49514.56/min [1200000], rate=49861.50/min [1210000], rate=50138.12/min [1220000], rate=50274.73/min [1230000], rate=50547.95/min [1240000], rate=50924.02/min [1250000], rate=51159.62/min [1260000], rate=51463.58/min [1270000], rate=51626.02/min [1280000], rate=51821.86/min [1290000], rate=51841.93/min [1300000], rate=51792.83/min [1310000], rate=51507.21/min [1320000], rate=51629.73/min [1330000], rate=51953.12/min [1340000], rate=52275.68/min [1350000], rate=51823.42/min [1360000], rate=51776.65/min [1370000], rate=51698.11/min [1380000], rate=51685.39/min [1390000], rate=51513.28/min [1400000], rate=51094.89/min [1410000], rate=50537.63/min [1420000], rate=50117.65/min [1430000], rate=49566.72/min [1440000], rate=48951.84/min [1450000], rate=49041.71/min [1460000], rate=49185.85/min [1470000], rate=49246.23/min [1480000], rate=49278.58/min [1490000], rate=49337.75/min [1500000], rate=49369.17/min [1510000], rate=49454.15/min [1520000], rate=49565.22/min [1530000], rate=49621.62/min [1540000], rate=49730.89/min [1550000], rate=49839.23/min [1560000], rate=49946.64/min [1570000], rate=50053.13/min [1580000], rate=50158.73/min [1590000], rate=50236.97/min [1600000], rate=50367.26/min [1610000], rate=50443.86/min [1620000], rate=49718.67/min [1630000], rate=49219.93/min [1640000], rate=48857.99/min [1650000], rate=48458.15/min [1660000], rate=48069.50/min [1670000], rate=47988.51/min [1680000], rate=47346.17/min [1690000], rate=47031.54/min [1700000], rate=46575.34/min [1710000], rate=46070.95/min [1720000], rate=45643.52/min [1730000], rate=45150.07/min [1740000], rate=44768.44/min [1750000], rate=44510.39/min [1760000], rate=44388.40/min [1770000], rate=44305.38/min [1780000], rate=44223.60/min [1790000], rate=43998.36/min [1800000], rate=43724.70/min [1810000], rate=43509.62/min [1820000], rate=43505.98/min [1830000], rate=43502.38/min [1840000], rate=43498.82/min [1850000], rate=43529.41/min [1860000], rate=43559.72/min [1870000], rate=43623.64/min [1880000], rate=43687.06/min [1890000], rate=43783.78/min [1900000], rate=43913.71/min [1910000], rate=44026.12/min [1920000], rate=44171.78/min [1930000], rate=44299.92/min [1940000], rate=44393.59/min [1950000], rate=44184.29/min -building interval tree based on /tmp/nxf.ZKvbNRKf7e/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=33333.33/min [20000], rate=36363.64/min [30000], rate=36734.69/min [40000], rate=32432.43/min [50000], rate=33707.87/min [60000], rate=35643.56/min [70000], rate=37500.00/min [80000], rate=39024.39/min [90000], rate=40298.51/min [100000], rate=41666.67/min [110000], rate=42857.14/min [120000], rate=44171.78/min [130000], rate=45348.84/min [140000], rate=46408.84/min [150000], rate=47619.05/min [160000], rate=48484.85/min [170000], rate=47222.22/min [180000], rate=45762.71/min [190000], rate=45418.33/min [200000], rate=44943.82/min [210000], rate=44055.94/min [220000], rate=43564.36/min [230000], rate=42990.65/min [240000], rate=42985.07/min [250000], rate=43103.45/min [260000], rate=42857.14/min [270000], rate=43085.11/min [280000], rate=42639.59/min [290000], rate=43069.31/min [300000], rate=43583.54/min [310000], rate=43559.72/min [320000], rate=44036.70/min [330000], rate=44494.38/min [340000], rate=44933.92/min [350000], rate=45356.37/min [360000], rate=45859.87/min [370000], rate=46153.85/min [380000], rate=46530.61/min [390000], rate=46893.79/min [400000], rate=47244.09/min [410000], rate=47036.33/min [420000], rate=47457.63/min [430000], rate=47866.42/min [440000], rate=48351.65/min [450000], rate=48736.46/min [460000], rate=49197.86/min [470000], rate=49214.66/min [480000], rate=48648.65/min [490000], rate=48196.72/min [500000], rate=47846.89/min [510000], rate=47589.42/min [520000], rate=47560.98/min [530000], rate=47533.63/min [540000], rate=47507.33/min [550000], rate=47482.01/min [560000], rate=47457.63/min [570000], rate=47500.00/min [580000], rate=47671.23/min [590000], rate=47644.68/min [600000], rate=47493.40/min [610000], rate=47225.81/min [620000], rate=47088.61/min [630000], rate=47191.01/min [640000], rate=46658.57/min [650000], rate=46428.57/min [660000], rate=45727.48/min [670000], rate=45785.88/min [680000], rate=45791.25/min [690000], rate=45898.00/min [700000], rate=46002.19/min [710000], rate=45905.17/min [720000], rate=45908.61/min [730000], rate=46008.40/min [740000], rate=45915.20/min [750000], rate=46106.56/min [760000], rate=46341.46/min [770000], rate=46525.68/min [780000], rate=46753.25/min [790000], rate=46837.94/min [800000], rate=47058.82/min [810000], rate=46775.75/min [820000], rate=46371.35/min [830000], rate=46111.11/min [840000], rate=45901.64/min [850000], rate=45698.92/min [860000], rate=45302.90/min [870000], rate=44312.39/min [880000], rate=43492.59/min [890000], rate=43309.00/min [900000], rate=43027.89/min [910000], rate=42924.53/min [920000], rate=42559.75/min [930000], rate=42369.02/min [940000], rate=42406.02/min [950000], rate=42505.59/min [960000], rate=42477.88/min [970000], rate=42574.98/min [980000], rate=42608.70/min [990000], rate=42611.19/min [1000000], rate=42704.63/min [1010000], rate=42676.06/min [1020000], rate=42767.30/min [1030000], rate=42886.88/min [1040000], rate=43064.18/min [1050000], rate=43328.75/min [1060000], rate=43561.64/min [1070000], rate=43822.53/min [1080000], rate=44051.67/min [1090000], rate=44278.94/min [1100000], rate=44474.39/min [1110000], rate=44697.99/min [1120000], rate=44949.83/min [1130000], rate=45200.00/min [1140000], rate=45418.33/min [1150000], rate=45634.92/min [1160000], rate=45849.80/min [1170000], rate=46032.79/min [1180000], rate=46033.81/min [1190000], rate=46243.52/min [1200000], rate=46451.61/min [1210000], rate=46628.13/min [1220000], rate=46743.30/min [1230000], rate=46857.14/min [1240000], rate=46910.47/min [1250000], rate=46963.06/min [1260000], rate=46985.71/min [1270000], rate=46691.18/min [1280000], rate=46265.06/min [1290000], rate=46181.38/min [1300000], rate=46345.81/min [1310000], rate=46481.37/min [1320000], rate=46615.66/min [1330000], rate=46748.68/min [1340000], rate=46260.07/min [1350000], rate=44554.46/min [1360000], rate=43823.85/min [1370000], rate=42969.16/min [1380000], rate=42746.52/min [1390000], rate=42638.04/min [1400000], rate=42617.96/min [1410000], rate=42131.47/min [1420000], rate=41703.38/min [1430000], rate=41610.09/min [1440000], rate=41399.14/min [1450000], rate=41349.81/min [1460000], rate=41126.76/min [1470000], rate=40757.86/min [1480000], rate=40510.95/min [1490000], rate=40470.80/min [1500000], rate=40577.10/min [1510000], rate=40737.41/min [1520000], rate=40896.86/min [1530000], rate=41037.10/min [1540000], rate=41158.13/min [1550000], rate=41132.24/min [1560000], rate=40944.88/min [1570000], rate=40761.58/min [1580000], rate=40495.51/min [1590000], rate=40253.16/min [1600000], rate=40167.36/min [1610000], rate=40166.32/min [1620000], rate=40148.70/min [1630000], rate=40147.78/min [1640000], rate=40179.67/min [1650000], rate=40211.21/min [1660000], rate=40258.69/min [1670000], rate=40321.93/min [1680000], rate=40400.80/min [1690000], rate=40462.89/min [1700000], rate=40540.54/min [1710000], rate=40617.58/min [1720000], rate=40710.06/min [1730000], rate=40817.93/min [1740000], rate=40909.09/min [1750000], rate=41031.65/min [1760000], rate=41137.51/min [1770000], rate=41242.72/min [1780000], rate=41283.34/min [1790000], rate=41275.94/min [1800000], rate=41268.63/min [1810000], rate=41277.08/min [1820000], rate=41301.06/min [1830000], rate=41324.80/min [1840000], rate=41379.31/min [1850000], rate=41433.37/min [1860000], rate=41486.99/min [1870000], rate=41555.56/min [1880000], rate=41608.26/min [1890000], rate=41675.85/min [1900000], rate=41758.24/min [1910000], rate=41840.09/min [1920000], rate=41936.66/min [1930000], rate=42047.93/min [1940000], rate=42158.64/min [1950000], rate=42238.27/min -building interval tree based on /tmp/nxf.ZKvbNRKf7e/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=42857.14/min [20000], rate=46153.85/min [30000], rate=47368.42/min [40000], rate=48000.00/min [50000], rate=48387.10/min [60000], rate=48000.00/min [70000], rate=47191.01/min [80000], rate=48000.00/min [90000], rate=49090.91/min [100000], rate=50000.00/min [110000], rate=51162.79/min [120000], rate=52173.91/min [130000], rate=53793.10/min [140000], rate=54901.96/min [150000], rate=55900.62/min [160000], rate=55813.95/min [170000], rate=51256.28/min [180000], rate=46153.85/min [190000], rate=43678.16/min [200000], rate=42105.26/min [210000], rate=40776.70/min [220000], rate=39639.64/min [230000], rate=39093.48/min [240000], rate=38709.68/min [250000], rate=38265.31/min [260000], rate=38518.52/min [270000], rate=38297.87/min [280000], rate=38181.82/min [290000], rate=37662.34/min [300000], rate=37422.04/min [310000], rate=37500.00/min [320000], rate=37573.39/min [330000], rate=37786.26/min [340000], rate=37988.83/min [350000], rate=38321.17/min [360000], rate=38502.67/min [370000], rate=38811.19/min [380000], rate=39108.06/min [390000], rate=39460.37/min [400000], rate=39801.00/min [410000], rate=40261.87/min [420000], rate=40579.71/min [430000], rate=40822.78/min [440000], rate=41250.00/min [450000], rate=41666.67/min [460000], rate=42201.83/min [470000], rate=42662.63/min [480000], rate=43113.77/min [490000], rate=43362.83/min [500000], rate=43541.36/min [510000], rate=43776.82/min [520000], rate=44067.80/min [530000], rate=44351.46/min [540000], rate=44628.10/min [550000], rate=44654.94/min [560000], rate=44979.92/min [570000], rate=44881.89/min [580000], rate=44501.28/min [590000], rate=44416.56/min [600000], rate=44389.64/min [610000], rate=44363.64/min [620000], rate=44233.06/min [630000], rate=44314.19/min [640000], rate=44444.44/min [650000], rate=44622.43/min [660000], rate=44847.11/min [670000], rate=45067.26/min [680000], rate=45232.82/min [690000], rate=45494.51/min [700000], rate=45701.85/min [710000], rate=45954.69/min [720000], rate=46104.59/min [730000], rate=46105.26/min [740000], rate=46298.23/min [750000], rate=45918.37/min [760000], rate=45783.13/min [770000], rate=45697.33/min [780000], rate=45658.54/min [790000], rate=45620.79/min [800000], rate=45584.05/min [810000], rate=45590.99/min [820000], rate=45640.07/min [830000], rate=45730.03/min [840000], rate=45818.18/min [850000], rate=45945.95/min [860000], rate=46071.43/min [870000], rate=46235.61/min [880000], rate=46397.19/min [890000], rate=46678.32/min [900000], rate=46875.00/min [910000], rate=47109.58/min [920000], rate=47219.85/min [930000], rate=46655.52/min [940000], rate=46229.51/min [950000], rate=45967.74/min [960000], rate=45714.29/min [970000], rate=45397.82/min [980000], rate=45196.00/min [990000], rate=45136.78/min [1000000], rate=45011.25/min [1010000], rate=44888.89/min [1020000], rate=44868.04/min [1030000], rate=44815.08/min [1040000], rate=44763.27/min [1050000], rate=44871.79/min [1060000], rate=44851.90/min [1070000], rate=44863.73/min [1080000], rate=44937.59/min [1090000], rate=44948.45/min [1100000], rate=44928.52/min [1110000], rate=44939.27/min [1120000], rate=45010.05/min [1130000], rate=45079.79/min [1140000], rate=45148.51/min [1150000], rate=45098.04/min [1160000], rate=45194.81/min [1170000], rate=45261.12/min [1180000], rate=45268.54/min [1190000], rate=45247.15/min [1200000], rate=45254.56/min [1210000], rate=45290.08/min [1220000], rate=45325.08/min [1230000], rate=45415.38/min [1240000], rate=45532.44/min [1250000], rate=45703.84/min [1260000], rate=45818.18/min [1270000], rate=45931.28/min [1280000], rate=46126.13/min [1290000], rate=46264.20/min [1300000], rate=46290.80/min [1310000], rate=45724.26/min [1320000], rate=45179.69/min [1330000], rate=44235.03/min [1340000], rate=43365.70/min [1350000], rate=42209.48/min [1360000], rate=41505.60/min [1370000], rate=40254.65/min [1380000], rate=39788.56/min [1390000], rate=39488.64/min [1400000], rate=39215.69/min [1410000], rate=38950.28/min [1420000], rate=38586.96/min [1430000], rate=38372.09/min [1440000], rate=38263.95/min [1450000], rate=38057.74/min [1460000], rate=37856.53/min [1470000], rate=37740.69/min [1480000], rate=37643.07/min [1490000], rate=37578.81/min [1500000], rate=37578.29/min [1510000], rate=37624.58/min [1520000], rate=37561.78/min [1530000], rate=37393.08/min [1540000], rate=37408.91/min [1550000], rate=37454.69/min [1560000], rate=37484.98/min [1570000], rate=37485.08/min [1580000], rate=37485.17/min [1590000], rate=37485.27/min [1600000], rate=37441.50/min [1610000], rate=37427.35/min [1620000], rate=37442.22/min [1630000], rate=37500.00/min [1640000], rate=37542.92/min [1650000], rate=37613.98/min [1660000], rate=37684.45/min [1670000], rate=37754.33/min [1680000], rate=37837.84/min [1690000], rate=37920.72/min [1700000], rate=38017.14/min [1710000], rate=38112.93/min [1720000], rate=38208.07/min [1730000], rate=38302.58/min [1740000], rate=38410.60/min [1750000], rate=38461.54/min [1760000], rate=38512.04/min [1770000], rate=38590.12/min [1780000], rate=38639.65/min [1790000], rate=38716.65/min [1800000], rate=38807.04/min [1810000], rate=38896.85/min [1820000], rate=38778.41/min [1830000], rate=38418.47/min [1840000], rate=38134.72/min [1850000], rate=37871.03/min [1860000], rate=37639.12/min [1870000], rate=37462.44/min [1880000], rate=37301.59/min [1890000], rate=37131.63/min [1900000], rate=37037.04/min [1910000], rate=36932.00/min [1920000], rate=36840.42/min [1930000], rate=36773.58/min [1940000], rate=36742.42/min