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/ea/428230b0a49670853cb2dc40778a31/SkinN_FFPE_L08_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/90feaf8bc485650506e1981959c788/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/428230b0a49670853cb2dc40778a31/SkinN_FFPE_L08_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/73670922ccc5b13afacdc412e52caa/SkinN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/90feaf8bc485650506e1981959c788/.command.run ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.sFcDrj6eoQ/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary -sample contains 67574114 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir -J /tmp/nxf.sFcDrj6eoQ/SkinN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.sFcDrj6eoQ/SkinN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=28571.43/min [20000], rate=20000.00/min [30000], rate=21686.75/min [40000], rate=23762.38/min [50000], rate=26086.96/min [60000], rate=26666.67/min [70000], rate=27631.58/min [80000], rate=29629.63/min [90000], rate=31213.87/min [100000], rate=32085.56/min [110000], rate=33502.54/min [120000], rate=33962.26/min [130000], rate=33620.69/min [140000], rate=34567.90/min [150000], rate=35294.12/min [160000], rate=36090.23/min [170000], rate=37090.91/min [180000], rate=38434.16/min [190000], rate=40282.69/min [200000], rate=40677.97/min [210000], rate=40384.62/min [220000], rate=41250.00/min [230000], rate=42331.29/min [240000], rate=43504.53/min [250000], rate=44378.70/min [260000], rate=44192.63/min [270000], rate=44505.49/min [280000], rate=44680.85/min [290000], rate=44274.81/min [300000], rate=44334.98/min [310000], rate=44711.54/min [320000], rate=44859.81/min [330000], rate=45308.92/min [340000], rate=45842.70/min [350000], rate=46666.67/min [360000], rate=47161.57/min [370000], rate=47741.94/min [380000], rate=48000.00/min [390000], rate=48953.97/min [400000], rate=50104.38/min [410000], rate=50931.68/min [420000], rate=51958.76/min [430000], rate=52977.41/min [440000], rate=53987.73/min [450000], rate=55102.04/min [460000], rate=56211.81/min [470000], rate=57200.81/min [480000], rate=58299.60/min [490000], rate=59393.94/min [500000], rate=60606.06/min [510000], rate=61693.55/min [520000], rate=62776.66/min [530000], rate=63855.42/min [540000], rate=65060.24/min [550000], rate=66132.26/min [560000], rate=67200.00/min [570000], rate=68127.49/min [580000], rate=69184.89/min [590000], rate=70238.10/min [600000], rate=70866.14/min [610000], rate=71206.23/min [620000], rate=72093.02/min [630000], rate=72552.78/min [640000], rate=72589.79/min [650000], rate=72625.70/min [660000], rate=72928.18/min [670000], rate=73090.91/min [680000], rate=73249.55/min [690000], rate=73665.48/min [700000], rate=74336.28/min [710000], rate=74345.55/min [720000], rate=73972.60/min [730000], rate=73737.37/min [740000], rate=74371.86/min [750000], rate=75000.00/min [760000], rate=75747.51/min [770000], rate=76490.07/min [780000], rate=77355.37/min [790000], rate=78217.82/min [800000], rate=78688.52/min [810000], rate=79541.73/min [820000], rate=79099.68/min [830000], rate=78178.96/min [840000], rate=78260.87/min [850000], rate=77743.90/min [860000], rate=76900.15/min [870000], rate=75982.53/min [880000], rate=76411.00/min [890000], rate=77056.28/min [900000], rate=77253.22/min [910000], rate=77446.81/min [920000], rate=78186.97/min [930000], rate=78151.26/min [940000], rate=78116.34/min [950000], rate=78404.40/min [960000], rate=78154.68/min [970000], rate=78225.81/min [980000], rate=78295.61/min [990000], rate=77647.06/min [1000000], rate=78125.00/min [1010000], rate=78701.30/min [1020000], rate=79274.61/min [1030000], rate=79948.25/min [1040000], rate=80516.13/min [1050000], rate=81185.57/min [1060000], rate=81853.28/min [1070000], rate=82413.35/min [1080000], rate=83076.92/min [1090000], rate=83738.80/min [1100000], rate=84398.98/min [1110000], rate=85057.47/min [1120000], rate=85714.29/min [1130000], rate=86369.43/min [1140000], rate=87133.76/min [1150000], rate=87786.26/min [1160000], rate=88324.87/min [1170000], rate=88860.76/min [1180000], rate=89393.94/min [1190000], rate=90037.83/min [1200000], rate=90452.26/min [1210000], rate=89740.42/min [1220000], rate=89926.29/min [1230000], rate=90552.15/min [1240000], rate=90400.97/min [1250000], rate=90144.23/min [1260000], rate=90214.80/min [1270000], rate=89858.49/min [1280000], rate=89929.74/min [1290000], rate=90104.77/min [1300000], rate=90487.24/min [1310000], rate=90657.44/min [1320000], rate=90514.29/min [1330000], rate=90373.73/min [1340000], rate=90744.92/min [1350000], rate=91113.61/min [1360000], rate=91582.49/min [1370000], rate=92152.47/min [1380000], rate=92617.45/min [1390000], rate=92769.74/min [1400000], rate=92613.01/min [1410000], rate=92056.58/min [1420000], rate=91318.33/min [1430000], rate=90506.33/min [1440000], rate=90187.89/min [1450000], rate=90248.96/min [1460000], rate=90589.45/min [1470000], rate=90834.19/min [1480000], rate=90243.90/min [1490000], rate=90577.51/min [1500000], rate=90725.81/min [1510000], rate=90600.00/min [1520000], rate=90566.04/min [1530000], rate=90354.33/min [1540000], rate=89883.27/min [1550000], rate=89509.14/min [1560000], rate=89741.13/min [1570000], rate=89885.50/min [1580000], rate=90199.81/min [1590000], rate=90340.91/min [1600000], rate=90395.48/min [1610000], rate=90364.83/min [1620000], rate=90671.64/min [1630000], rate=91061.45/min [1640000], rate=91534.88/min [1650000], rate=92007.43/min [1660000], rate=92479.11/min [1670000], rate=92949.91/min [1680000], rate=93419.83/min [1690000], rate=93888.89/min [1700000], rate=94095.94/min -building interval tree based on /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=66666.67/min [30000], rate=66666.67/min [40000], rate=60000.00/min [50000], rate=58823.53/min [60000], rate=61016.95/min [70000], rate=65625.00/min [80000], rate=65753.42/min [90000], rate=63529.41/min [100000], rate=69767.44/min [110000], rate=71739.13/min [120000], rate=72727.27/min [130000], rate=75728.16/min [140000], rate=77777.78/min [150000], rate=78947.37/min [160000], rate=76190.48/min [170000], rate=78461.54/min [180000], rate=80000.00/min [190000], rate=83823.53/min [200000], rate=85106.38/min [210000], rate=82352.94/min [220000], rate=79518.07/min [230000], rate=81656.80/min [240000], rate=84210.53/min [250000], rate=87209.30/min [260000], rate=90697.67/min [270000], rate=93103.45/min [280000], rate=93333.33/min [290000], rate=93048.13/min [300000], rate=93264.25/min [310000], rate=90731.71/min [320000], rate=90140.85/min [330000], rate=87610.62/min [340000], rate=89082.97/min [350000], rate=90128.76/min [360000], rate=90000.00/min [370000], rate=91358.02/min [380000], rate=93442.62/min [390000], rate=93600.00/min [400000], rate=93023.26/min [410000], rate=93893.13/min [420000], rate=94736.84/min [430000], rate=94505.49/min [440000], rate=94964.03/min [450000], rate=95070.42/min [460000], rate=95833.33/min [470000], rate=96575.34/min [480000], rate=95681.06/min [490000], rate=93929.71/min [500000], rate=93167.70/min [510000], rate=93865.03/min [520000], rate=95412.84/min [530000], rate=96951.22/min [540000], rate=98480.24/min [550000], rate=99099.10/min [560000], rate=99408.28/min [570000], rate=97994.27/min [580000], rate=94822.89/min [590000], rate=87407.41/min [600000], rate=81447.96/min [610000], rate=79220.78/min [620000], rate=80345.57/min [630000], rate=81290.32/min [640000], rate=81876.33/min [650000], rate=82452.43/min [660000], rate=83720.93/min [670000], rate=83575.88/min [680000], rate=83778.23/min [690000], rate=84489.80/min [700000], rate=85192.70/min [710000], rate=85370.74/min [720000], rate=85544.55/min [730000], rate=84393.06/min [740000], rate=83615.82/min [750000], rate=83487.94/min [760000], rate=83516.48/min [770000], rate=83544.30/min [780000], rate=82978.72/min [790000], rate=82149.05/min [800000], rate=82758.62/min [810000], rate=82793.87/min [820000], rate=83108.11/min [830000], rate=83557.05/min [840000], rate=83860.23/min [850000], rate=84158.42/min [860000], rate=84039.09/min [870000], rate=84193.55/min [880000], rate=84615.38/min [890000], rate=85303.51/min [900000], rate=85987.26/min [910000], rate=86392.41/min [920000], rate=87066.25/min [930000], rate=86915.89/min [940000], rate=87171.56/min [950000], rate=87423.31/min [960000], rate=87938.93/min [970000], rate=88181.82/min [980000], rate=88288.29/min [990000], rate=88392.86/min [1000000], rate=88626.29/min [1010000], rate=89117.65/min [1020000], rate=89604.69/min [1030000], rate=89956.33/min [1040000], rate=90303.91/min [1050000], rate=90517.24/min [1060000], rate=91248.21/min [1070000], rate=91583.45/min [1080000], rate=85601.06/min [1090000], rate=81242.24/min [1100000], rate=76477.40/min [1110000], rate=72549.02/min [1120000], rate=70000.00/min [1130000], rate=67529.88/min [1140000], rate=65580.06/min [1150000], rate=64126.39/min [1160000], rate=62702.70/min [1170000], rate=61578.95/min [1180000], rate=60461.14/min [1190000], rate=59699.00/min [1200000], rate=58919.80/min [1210000], rate=58407.08/min [1220000], rate=58095.24/min [1230000], rate=57746.48/min [1240000], rate=57407.41/min [1250000], rate=57034.22/min [1260000], rate=56629.21/min [1270000], rate=56194.69/min [1280000], rate=55611.88/min [1290000], rate=55444.13/min [1300000], rate=55007.05/min [1310000], rate=54621.26/min [1320000], rate=54620.69/min [1330000], rate=54657.53/min [1340000], rate=54656.70/min [1350000], rate=54582.21/min [1360000], rate=54655.06/min [1370000], rate=54836.56/min [1380000], rate=55016.61/min [1390000], rate=55158.73/min [1400000], rate=55335.97/min [1410000], rate=55258.00/min [1420000], rate=55217.11/min [1430000], rate=55176.85/min [1440000], rate=55137.20/min [1450000], rate=54889.59/min [1460000], rate=54921.63/min [1470000], rate=54953.27/min [1480000], rate=54882.57/min [1490000], rate=54880.29/min [1500000], rate=54844.61/min [1510000], rate=54975.73/min [1520000], rate=54906.68/min [1530000], rate=55068.99/min [1540000], rate=55131.26/min [1550000], rate=55258.47/min [1560000], rate=55450.24/min [1570000], rate=54959.16/min [1580000], rate=54639.77/min [1590000], rate=54545.45/min [1600000], rate=54237.29/min [1610000], rate=53876.19/min [1620000], rate=53583.24/min [1630000], rate=53355.16/min [1640000], rate=53246.75/min [1650000], rate=53083.11/min [1660000], rate=52950.56/min [1670000], rate=52848.10/min [1680000], rate=52747.25/min -building interval tree based on /tmp/nxf.sFcDrj6eoQ/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=52173.91/min [30000], rate=56250.00/min [40000], rate=60000.00/min [50000], rate=58823.53/min [60000], rate=56250.00/min [70000], rate=54545.45/min [80000], rate=51612.90/min [90000], rate=50467.29/min [100000], rate=51724.14/min [110000], rate=51562.50/min [120000], rate=52173.91/min [130000], rate=51655.63/min [140000], rate=53164.56/min [150000], rate=48387.10/min [160000], rate=43835.62/min [170000], rate=42323.65/min [180000], rate=41698.84/min [190000], rate=40425.53/min [200000], rate=40133.78/min [210000], rate=37837.84/min [220000], rate=36666.67/min [230000], rate=36315.79/min [240000], rate=36641.22/min [250000], rate=37037.04/min [260000], rate=36966.82/min [270000], rate=36080.18/min [280000], rate=36363.64/min [290000], rate=36631.58/min [300000], rate=36885.25/min [310000], rate=37274.55/min [320000], rate=37209.30/min [330000], rate=37500.00/min [340000], rate=38130.84/min [350000], rate=39179.10/min [360000], rate=39705.88/min [370000], rate=39361.70/min [380000], rate=39175.26/min [390000], rate=39130.43/min [400000], rate=39408.87/min [410000], rate=39549.84/min [420000], rate=39685.04/min [430000], rate=39876.35/min [440000], rate=40121.58/min [450000], rate=40000.00/min [460000], rate=40116.28/min [470000], rate=40343.35/min [480000], rate=40677.97/min [490000], rate=40720.22/min [500000], rate=40431.27/min [510000], rate=40210.25/min [520000], rate=40258.06/min [530000], rate=39949.75/min [540000], rate=40000.00/min [550000], rate=40000.00/min [560000], rate=39904.99/min [570000], rate=39767.44/min [580000], rate=40046.03/min [590000], rate=40273.04/min [600000], rate=40404.04/min [610000], rate=40397.35/min [620000], rate=40744.80/min [630000], rate=40953.41/min [640000], rate=41113.49/min [650000], rate=41445.27/min [660000], rate=41684.21/min [670000], rate=42182.58/min [680000], rate=42455.78/min [690000], rate=42461.54/min [700000], rate=42253.52/min [710000], rate=42178.22/min [720000], rate=42023.35/min [730000], rate=41913.88/min [740000], rate=41729.32/min [750000], rate=41589.65/min [760000], rate=41605.84/min [770000], rate=41659.15/min [780000], rate=41711.23/min [790000], rate=41872.79/min [800000], rate=42031.52/min [810000], rate=42187.50/min [820000], rate=42413.79/min [830000], rate=42710.12/min [840000], rate=43150.68/min [850000], rate=43589.74/min [860000], rate=43877.55/min [870000], rate=44162.44/min [880000], rate=44444.44/min [890000], rate=44723.62/min [900000], rate=45037.53/min [910000], rate=44901.32/min [920000], rate=44624.09/min [930000], rate=44497.61/min [940000], rate=44479.50/min [950000], rate=44496.49/min [960000], rate=44307.69/min [970000], rate=44597.70/min [980000], rate=44748.86/min [990000], rate=44695.26/min [1000000], rate=44642.86/min [1010000], rate=44591.61/min [1020000], rate=44638.95/min [1030000], rate=44524.50/min [1040000], rate=44412.81/min [1050000], rate=44554.46/min [1060000], rate=44662.92/min [1070000], rate=44769.87/min [1080000], rate=44906.44/min [1090000], rate=45072.36/min [1100000], rate=45267.49/min [1110000], rate=45491.80/min [1120000], rate=45807.77/min [1130000], rate=45966.10/min [1140000], rate=46185.01/min [1150000], rate=46122.99/min [1160000], rate=46092.72/min [1170000], rate=46123.52/min [1180000], rate=46033.81/min [1190000], rate=46005.15/min [1200000], rate=46035.81/min [1210000], rate=46124.52/min [1220000], rate=46241.31/min [1230000], rate=46385.92/min [1240000], rate=46558.20/min [1250000], rate=46758.10/min [1260000], rate=46927.37/min [1270000], rate=47095.18/min [1280000], rate=47232.47/min [1290000], rate=47223.92/min [1300000], rate=47158.40/min [1310000], rate=47094.07/min [1320000], rate=47030.88/min [1330000], rate=46996.47/min [1340000], rate=47045.06/min [1350000], rate=47147.85/min [1360000], rate=47113.16/min [1370000], rate=47214.24/min [1380000], rate=47233.31/min [1390000], rate=47305.73/min [1400000], rate=47350.62/min [1410000], rate=47635.14/min [1420000], rate=47945.98/min [1430000], rate=48256.47/min [1440000], rate=48566.61/min [1450000], rate=48848.96/min [1460000], rate=49075.63/min [1470000], rate=49218.75/min [1480000], rate=49388.21/min [1490000], rate=49584.03/min [1500000], rate=49641.48/min [1510000], rate=49616.65/min [1520000], rate=49646.16/min [1530000], rate=49783.08/min [1540000], rate=49757.67/min [1550000], rate=49706.04/min [1560000], rate=49787.23/min [1570000], rate=49867.65/min [1580000], rate=50000.00/min [1590000], rate=50131.37/min [1600000], rate=50288.11/min [1610000], rate=50443.86/min [1620000], rate=50625.00/min [1630000], rate=50910.98/min [1640000], rate=51170.05/min [1650000], rate=51428.57/min [1660000], rate=51606.22/min [1670000], rate=51782.95/min [1680000], rate=52039.24/min -building interval tree based on /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=27272.73/min [20000], rate=27906.98/min [30000], rate=26865.67/min [40000], rate=27906.98/min [50000], rate=30000.00/min [60000], rate=32727.27/min [70000], rate=34426.23/min [80000], rate=36090.23/min [90000], rate=37762.24/min [100000], rate=37267.08/min [110000], rate=35294.12/min [120000], rate=33488.37/min [130000], rate=32365.15/min [140000], rate=32432.43/min [150000], rate=33088.24/min [160000], rate=32876.71/min [170000], rate=32587.86/min [180000], rate=32432.43/min [190000], rate=32386.36/min [200000], rate=32786.89/min [210000], rate=33070.87/min [220000], rate=33759.59/min [230000], rate=34413.97/min [240000], rate=34782.61/min [250000], rate=35046.73/min [260000], rate=35056.18/min [270000], rate=35448.58/min [280000], rate=36129.03/min [290000], rate=36477.99/min [300000], rate=37113.40/min [310000], rate=37125.75/min [320000], rate=37209.30/min [330000], rate=37858.51/min [340000], rate=38490.57/min [350000], rate=39252.34/min [360000], rate=39852.40/min [370000], rate=40290.38/min [380000], rate=40353.98/min [390000], rate=40068.49/min [400000], rate=40066.78/min [410000], rate=40130.51/min [420000], rate=39747.63/min [430000], rate=40000.00/min [440000], rate=40490.80/min [450000], rate=40847.20/min [460000], rate=41441.44/min [470000], rate=41777.78/min [480000], rate=42352.94/min [490000], rate=42982.46/min [500000], rate=43795.62/min [510000], rate=44541.48/min [520000], rate=44635.19/min [530000], rate=44475.52/min [540000], rate=44383.56/min [550000], rate=44414.54/min [560000], rate=44503.31/min [570000], rate=44940.87/min [580000], rate=45490.20/min [590000], rate=45618.56/min [600000], rate=45397.23/min [610000], rate=45409.43/min [620000], rate=45588.24/min [630000], rate=45762.71/min [640000], rate=46043.17/min [650000], rate=46263.35/min [660000], rate=46808.51/min [670000], rate=47072.60/min [680000], rate=47386.76/min [690000], rate=46938.78/min [700000], rate=46204.62/min [710000], rate=46557.38/min [720000], rate=46956.52/min [730000], rate=47351.35/min [740000], rate=47537.47/min [750000], rate=46875.00/min [760000], rate=46578.14/min [770000], rate=46572.58/min [780000], rate=46613.55/min [790000], rate=46561.89/min [800000], rate=46601.94/min [810000], rate=46596.36/min [820000], rate=46502.84/min [830000], rate=46325.58/min [840000], rate=46153.85/min [850000], rate=46153.85/min [860000], rate=46112.60/min [870000], rate=46276.60/min [880000], rate=46153.85/min [890000], rate=46313.96/min [900000], rate=46312.18/min [910000], rate=46389.12/min [920000], rate=46347.61/min [930000], rate=46500.00/min [940000], rate=46534.65/min [950000], rate=46568.63/min [960000], rate=46677.47/min [970000], rate=46822.20/min [980000], rate=47002.40/min [990000], rate=47330.68/min [1000000], rate=47581.28/min [1010000], rate=47867.30/min [1020000], rate=48151.06/min [1030000], rate=47611.71/min [1040000], rate=46846.85/min [1050000], rate=46323.53/min [1060000], rate=45755.40/min [1070000], rate=45564.23/min [1080000], rate=45378.15/min [1090000], rate=45353.68/min [1100000], rate=45329.67/min [1110000], rate=45336.96/min [1120000], rate=45100.67/min [1130000], rate=45079.79/min [1140000], rate=45029.62/min [1150000], rate=45009.78/min [1160000], rate=45077.72/min [1170000], rate=45173.75/min [1180000], rate=45153.06/min [1190000], rate=45047.32/min [1200000], rate=45112.78/min [1210000], rate=45261.85/min [1220000], rate=45269.02/min [1230000], rate=45331.70/min [1240000], rate=45448.99/min [1250000], rate=45482.11/min [1260000], rate=45624.62/min [1270000], rate=45683.45/min [1280000], rate=45878.14/min [1290000], rate=46181.38/min [1300000], rate=46483.91/min [1310000], rate=46813.58/min [1320000], rate=47114.81/min [1330000], rate=47359.05/min [1340000], rate=47489.66/min [1350000], rate=47619.05/min [1360000], rate=47775.18/min [1370000], rate=47902.10/min [1380000], rate=47477.06/min [1390000], rate=47198.64/min [1400000], rate=46822.74/min [1410000], rate=46585.90/min [1420000], rate=46329.53/min [1430000], rate=46178.69/min [1440000], rate=46376.81/min [1450000], rate=46153.85/min [1460000], rate=46032.58/min [1470000], rate=45961.44/min [1480000], rate=45844.09/min [1490000], rate=45658.84/min [1500000], rate=45685.28/min [1510000], rate=45642.32/min [1520000], rate=45737.21/min [1530000], rate=45785.54/min [1540000], rate=45856.08/min [1550000], rate=45925.93/min [1560000], rate=45995.09/min [1570000], rate=46086.11/min [1580000], rate=46108.95/min [1590000], rate=46176.19/min [1600000], rate=46198.27/min [1610000], rate=46264.37/min [1620000], rate=46219.69/min [1630000], rate=45872.42/min [1640000], rate=45576.66/min [1650000], rate=45288.20/min [1660000], rate=45108.70/min [1670000], rate=44993.26/min [1680000], rate=44859.81/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir --filt_file /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.sFcDrj6eoQ/./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... 10500000.00 reads per min processed... 12000000.00 reads per min processed... 10800000.00 reads per min processed... 10000000.00 reads per min processed... 8250000.00 reads per min processed... 8000000.00 reads per min processed... 7090909.09 reads per min processed... 7000000.00 reads per min processed... 6923076.92 reads per min processed... 6400000.00 reads per min processed... 6375000.00 reads per min processed... 6352941.18 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 5727272.73 reads per min processed... 5739130.43 reads per min processed... 5520000.00 reads per min processed... 5333333.33 reads per min processed... 5357142.86 reads per min processed... 5200000.00 reads per min processed... 5225806.45 reads per min processed... 5250000.00 reads per min processed... 5272727.27 reads per min processed... 5294117.65 reads per min processed... 5166666.67 reads per min processed... 5189189.19 reads per min processed... 5210526.32 reads per min processed... 5368421.05 reads per min processed... 5384615.38 reads per min processed... 5538461.54 reads per min processed... 5550000.00 reads per min processed... 5560975.61 reads per min processed... 5707317.07 reads per min processed... 5714285.71 reads per min processed... 5857142.86 reads per min processed... 5860465.12 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 6136363.64 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... 5884615.38 reads per min processed... 5886792.45 reads per min processed... 5888888.89 reads per min processed... 5890909.09 reads per min processed... 5892857.14 reads per min processed... 5894736.84 reads per min processed... 5796610.17 reads per min processed... 5800000.00 reads per min processed... 5803278.69 reads per min processed... 5806451.61 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.sFcDrj6eoQ/SkinN_FFPE_L08_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.sFcDrj6eoQ/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -85716.074422 EM: Round [1] log likelihood: -85411.466990 EM: Round [2] log likelihood: -85292.621071 EM: Round [3] log likelihood: -85236.050171 EM: Round [4] log likelihood: -85206.062043 EM: Round [5] log likelihood: -85189.199338 EM: Round [6] log likelihood: -85179.296949 EM: Round [7] log likelihood: -85173.238188 EM: Round [8] log likelihood: -85169.376563 EM: Round [9] log likelihood: -85166.816416 EM: Round [10] log likelihood: -85165.055831 EM: Round [11] log likelihood: -85163.804319 EM: Round [12] log likelihood: -85162.888075 EM: Round [13] log likelihood: -85162.199648 EM: Round [14] log likelihood: -85161.670509 EM: Round [15] log likelihood: -85161.255656 EM: Round [16] log likelihood: -85160.924726 EM: Round [17] log likelihood: -85160.656723 EM: Round [18] log likelihood: -85160.436792 EM: Round [19] log likelihood: -85160.254204 EM: Round [20] log likelihood: -85160.101062 EM: Round [21] log likelihood: -85159.971453 EM: Round [22] log likelihood: -85159.860879 EM: Round [23] log likelihood: -85159.765869 EM: Round [24] log likelihood: -85159.683707 EM: Round [25] log likelihood: -85159.612246 EM: Round [26] log likelihood: -85159.549765 EM: Round [27] log likelihood: -85159.494876 EM: Round [28] log likelihood: -85159.446446 EM: Round [29] log likelihood: -85159.403541 EM: Round [30] log likelihood: -85159.365391 EM: Round [31] log likelihood: -85159.331350 EM: Round [32] log likelihood: -85159.300879 EM: Round [33] log likelihood: -85159.273519 EM: Round [34] log likelihood: -85159.248883 EM: Round [35] log likelihood: -85159.226641 EM: Round [36] log likelihood: -85159.206509 EM: Round [37] log likelihood: -85159.188242 EM: Round [38] log likelihood: -85159.171630 EM: Round [39] log likelihood: -85159.156491 EM: Round [40] log likelihood: -85159.142664 EM: Round [41] log likelihood: -85159.130012 EM: Round [42] log likelihood: -85159.118413 EM: Round [43] log likelihood: -85159.107759 EM: Round [44] log likelihood: -85159.097957 EM: Round [45] log likelihood: -85159.088924 EM: Round [46] log likelihood: -85159.080586 EM: Round [47] log likelihood: -85159.072877 EM: Round [48] log likelihood: -85159.065741 EM: Round [49] log likelihood: -85159.059124 EM: Round [50] log likelihood: -85159.052980 EM: Round [51] log likelihood: -85159.047269 EM: Round [52] log likelihood: -85159.041952 EM: Round [53] log likelihood: -85159.036997 EM: Round [54] log likelihood: -85159.032373 EM: Round [55] log likelihood: -85159.028052 EM: Round [56] log likelihood: -85159.024011 EM: Round [57] log likelihood: -85159.020226 EM: Round [58] log likelihood: -85159.016679 EM: Round [59] log likelihood: -85159.013349 EM: Round [60] log likelihood: -85159.010222 EM: Round [61] log likelihood: -85159.007280 EM: Round [62] log likelihood: -85159.004511 EM: Round [63] log likelihood: -85159.001902 EM: Round [64] log likelihood: -85158.999441 EM: Round [65] log likelihood: -85158.997117 EM: Round [66] log likelihood: -85158.994921 EM: Round [67] log likelihood: -85158.992844 EM: Round [68] log likelihood: -85158.990877 EM: Round [69] log likelihood: -85158.989014 EM: Round [70] log likelihood: -85158.987246 EM: Round [71] log likelihood: -85158.985567 EM: Round [72] log likelihood: -85158.983972 EM: Round [73] log likelihood: -85158.982456 EM: Round [74] log likelihood: -85158.981012 EM: Round [75] log likelihood: -85158.979636 EM: Round [76] log likelihood: -85158.978325 EM: Round [77] log likelihood: -85158.977073 EM: Round [78] log likelihood: -85158.975878 EM: Round [79] log likelihood: -85158.974735 EM: Round [80] log likelihood: -85158.973642 EM: Round [81] log likelihood: -85158.972596 EM: Round [82] log likelihood: -85158.971593 EM: Round [83] log likelihood: -85158.970631 EM: Round [84] log likelihood: -85158.969708 EM: Round [85] log likelihood: -85158.968822 EM: Round [86] log likelihood: -85158.967970 EM: Round [87] log likelihood: -85158.967150 EM: Round [88] log likelihood: -85158.966361 EM: Round [89] log likelihood: -85158.965602 EM: Round [90] log likelihood: -85158.964869 EM: Round [91] log likelihood: -85158.964162 EM: Round [92] log likelihood: -85158.963480 EM: Round [93] log likelihood: -85158.962821 EM: Round [94] log likelihood: -85158.962184 EM: Round [95] log likelihood: -85158.961568 EM: Round [96] log likelihood: -85158.960972 EM: Round [97] log likelihood: -85158.960395 EM: Round [98] log likelihood: -85158.959835 EM: Round [99] log likelihood: -85158.959292 EM: Round [100] log likelihood: -85158.958766 EM: Round [101] log likelihood: -85158.958254 EM: Round [102] log likelihood: -85158.957758 EM: Round [103] log likelihood: -85158.957275 EM: Round [104] log likelihood: -85158.956806 EM: Round [105] log likelihood: -85158.956350 EM: Round [106] log likelihood: -85158.955905 EM: Round [107] log likelihood: -85158.955473 EM: Round [108] log likelihood: -85158.955051 EM: Round [109] log likelihood: -85158.954640 EM: Round [110] log likelihood: -85158.954239 EM: Round [111] log likelihood: -85158.953848 EM: Round [112] log likelihood: -85158.953466 EM: Round [113] log likelihood: -85158.953094 EM: Round [114] log likelihood: -85158.952729 EM: Round [115] log likelihood: -85158.952374 EM: Round [116] log likelihood: -85158.952026 EM: Round [117] log likelihood: -85158.951686 EM: Round [118] log likelihood: -85158.951353 EM: Round [119] log likelihood: -85158.951028 EM: Round [120] log likelihood: -85158.950709 EM: Round [121] log likelihood: -85158.950397 EM: Round [122] log likelihood: -85158.950091 EM: Round [123] log likelihood: -85158.949792 EM: Round [124] log likelihood: -85158.949498 EM: Round [125] log likelihood: -85158.949211 EM: Round [126] log likelihood: -85158.948929 EM: Round [127] log likelihood: -85158.948652 EM: Round [128] log likelihood: -85158.948381 EM: Round [129] log likelihood: -85158.948115 EM: Round [130] log likelihood: -85158.947853 EM: Round [131] log likelihood: -85158.947597 EM: Round [132] log likelihood: -85158.947345 EM: Round [133] log likelihood: -85158.947098 EM: Round [134] log likelihood: -85158.946855 EM: Round [135] log likelihood: -85158.946617 EM: Round [136] log likelihood: -85158.946382 EM: Round [137] log likelihood: -85158.946152 EM: Round [138] log likelihood: -85158.945926 EM: Round [139] log likelihood: -85158.945704 EM: Round [140] log likelihood: -85158.945485 EM: Round [141] log likelihood: -85158.945270 EM: Round [142] log likelihood: -85158.945059 EM: Round [143] log likelihood: -85158.944851 EM: Round [144] log likelihood: -85158.944647 EM: Round [145] log likelihood: -85158.944446 EM: Round [146] log likelihood: -85158.944248 EM: Round [147] log likelihood: -85158.944054 EM: Round [148] log likelihood: -85158.943862 EM: Round [149] log likelihood: -85158.943674 EM: Round [150] log likelihood: -85158.943489 EM: Round [151] log likelihood: -85158.943307 EM: Round [152] log likelihood: -85158.943127 EM: Round [153] log likelihood: -85158.942951 EM: Round [154] log likelihood: -85158.942777 EM: Round [155] log likelihood: -85158.942606 EM: Round [156] log likelihood: -85158.942437 EM: Round [157] log likelihood: -85158.942272 EM: Round [158] log likelihood: -85158.942108 EM: Round [159] log likelihood: -85158.941948 EM: Round [160] log likelihood: -85158.941789 EM: Round [161] log likelihood: -85158.941634 EM: Round [162] log likelihood: -85158.941480 EM: Round [163] log likelihood: -85158.941329 EM: Round [164] log likelihood: -85158.941180 EM: Round [165] log likelihood: -85158.941034 EM: Round [166] log likelihood: -85158.940890 EM: Round [167] log likelihood: -85158.940748 EM: Round [168] log likelihood: -85158.940608 EM: Round [169] log likelihood: -85158.940470 EM: Round [170] log likelihood: -85158.940334 EM: Round [171] log likelihood: -85158.940201 EM: Round [172] log likelihood: -85158.940069 EM: Round [173] log likelihood: -85158.939939 EM: Round [174] log likelihood: -85158.939811 EM: Round [175] log likelihood: -85158.939686 EM: Round [176] log likelihood: -85158.939562 EM: Round [177] log likelihood: -85158.939440 EM: Round [178] log likelihood: -85158.939319 EM: Round [179] log likelihood: -85158.939201 EM: Round [180] log likelihood: -85158.939084 EM: Round [181] log likelihood: -85158.938969 EM: Round [182] log likelihood: -85158.938856 EM: Round [183] log likelihood: -85158.938744 EM: Round [184] log likelihood: -85158.938634 EM: Round [185] log likelihood: -85158.938526 EM: Round [186] log likelihood: -85158.938419 EM: Round [187] log likelihood: -85158.938314 EM: Round [188] log likelihood: -85158.938211 EM: Round [189] log likelihood: -85158.938109 EM: Round [190] log likelihood: -85158.938008 EM: Round [191] log likelihood: -85158.937909 EM: Stopping iterations at round 191 due to insufficient improvement in likelihood. EM: Starting log likelihood: -85600.357800 EM: Round [1] log likelihood: -85335.974505 EM: Round [2] log likelihood: -85236.603303 EM: Round [3] log likelihood: -85190.298242 EM: Round [4] log likelihood: -85166.028822 EM: Round [5] log likelihood: -85152.456518 EM: Round [6] log likelihood: -85144.507818 EM: Round [7] log likelihood: -85139.653896 EM: Round [8] log likelihood: -85136.567657 EM: Round [9] log likelihood: -85134.528537 EM: Round [10] log likelihood: -85133.132459 EM: Round [11] log likelihood: -85132.145181 EM: Round [12] log likelihood: -85131.426351 EM: Round [13] log likelihood: -85130.889162 EM: Round [14] log likelihood: -85130.478302 EM: Round [15] log likelihood: -85130.157541 EM: Round [16] log likelihood: -85129.902530 EM: Round [17] log likelihood: -85129.696519 EM: Round [18] log likelihood: -85129.527725 EM: Round [19] log likelihood: -85129.387696 EM: Round [20] log likelihood: -85129.270250 EM: Round [21] log likelihood: -85129.170788 EM: Round [22] log likelihood: -85129.085833 EM: Round [23] log likelihood: -85129.012718 EM: Round [24] log likelihood: -85128.949365 EM: Round [25] log likelihood: -85128.894139 EM: Round [26] log likelihood: -85128.845735 EM: Round [27] log likelihood: -85128.803102 EM: Round [28] log likelihood: -85128.765384 EM: Round [29] log likelihood: -85128.731879 EM: Round [30] log likelihood: -85128.702005 EM: Round [31] log likelihood: -85128.675276 EM: Round [32] log likelihood: -85128.651285 EM: Round [33] log likelihood: -85128.629688 EM: Round [34] log likelihood: -85128.610193 EM: Round [35] log likelihood: -85128.592548 EM: Round [36] log likelihood: -85128.576540 EM: Round [37] log likelihood: -85128.561984 EM: Round [38] log likelihood: -85128.548719 EM: Round [39] log likelihood: -85128.536606 EM: Round [40] log likelihood: -85128.525523 EM: Round [41] log likelihood: -85128.515365 EM: Round [42] log likelihood: -85128.506037 EM: Round [43] log likelihood: -85128.497458 EM: Round [44] log likelihood: -85128.489554 EM: Round [45] log likelihood: -85128.482262 EM: Round [46] log likelihood: -85128.475524 EM: Round [47] log likelihood: -85128.469290 EM: Round [48] log likelihood: -85128.463514 EM: Round [49] log likelihood: -85128.458154 EM: Round [50] log likelihood: -85128.453176 EM: Round [51] log likelihood: -85128.448546 EM: Round [52] log likelihood: -85128.444235 EM: Round [53] log likelihood: -85128.440216 EM: Round [54] log likelihood: -85128.436466 EM: Round [55] log likelihood: -85128.432962 EM: Round [56] log likelihood: -85128.429685 EM: Round [57] log likelihood: -85128.426617 EM: Round [58] log likelihood: -85128.423743 EM: Round [59] log likelihood: -85128.421046 EM: Round [60] log likelihood: -85128.418514 EM: Round [61] log likelihood: -85128.416134 EM: Round [62] log likelihood: -85128.413896 EM: Round [63] log likelihood: -85128.411789 EM: Round [64] log likelihood: -85128.409802 EM: Round [65] log likelihood: -85128.407929 EM: Round [66] log likelihood: -85128.406161 EM: Round [67] log likelihood: -85128.404490 EM: Round [68] log likelihood: -85128.402910 EM: Round [69] log likelihood: -85128.401414 EM: Round [70] log likelihood: -85128.399998 EM: Round [71] log likelihood: -85128.398655 EM: Round [72] log likelihood: -85128.397381 EM: Round [73] log likelihood: -85128.396171 EM: Round [74] log likelihood: -85128.395021 EM: Round [75] log likelihood: -85128.393927 EM: Round [76] log likelihood: -85128.392886 EM: Round [77] log likelihood: -85128.391894 EM: Round [78] log likelihood: -85128.390949 EM: Round [79] log likelihood: -85128.390047 EM: Round [80] log likelihood: -85128.389185 EM: Round [81] log likelihood: -85128.388362 EM: Round [82] log likelihood: -85128.387575 EM: Round [83] log likelihood: -85128.386821 EM: Round [84] log likelihood: -85128.386099 EM: Round [85] log likelihood: -85128.385407 EM: Round [86] log likelihood: -85128.384744 EM: Round [87] log likelihood: -85128.384107 EM: Round [88] log likelihood: -85128.383495 EM: Round [89] log likelihood: -85128.382906 EM: Round [90] log likelihood: -85128.382340 EM: Round [91] log likelihood: -85128.381795 EM: Round [92] log likelihood: -85128.381270 EM: Round [93] log likelihood: -85128.380764 EM: Round [94] log likelihood: -85128.380275 EM: Round [95] log likelihood: -85128.379804 EM: Round [96] log likelihood: -85128.379348 EM: Round [97] log likelihood: -85128.378908 EM: Round [98] log likelihood: -85128.378482 EM: Round [99] log likelihood: -85128.378070 EM: Round [100] log likelihood: -85128.377671 EM: Round [101] log likelihood: -85128.377284 EM: Round [102] log likelihood: -85128.376909 EM: Round [103] log likelihood: -85128.376545 EM: Round [104] log likelihood: -85128.376191 EM: Round [105] log likelihood: -85128.375848 EM: Round [106] log likelihood: -85128.375514 EM: Round [107] log likelihood: -85128.375190 EM: Round [108] log likelihood: -85128.374874 EM: Round [109] log likelihood: -85128.374567 EM: Round [110] log likelihood: -85128.374268 EM: Round [111] log likelihood: -85128.373977 EM: Round [112] log likelihood: -85128.373693 EM: Round [113] log likelihood: -85128.373416 EM: Round [114] log likelihood: -85128.373146 EM: Round [115] log likelihood: -85128.372882 EM: Round [116] log likelihood: -85128.372624 EM: Round [117] log likelihood: -85128.372373 EM: Round [118] log likelihood: -85128.372127 EM: Round [119] log likelihood: -85128.371887 EM: Round [120] log likelihood: -85128.371652 EM: Round [121] log likelihood: -85128.371422 EM: Round [122] log likelihood: -85128.371197 EM: Round [123] log likelihood: -85128.370977 EM: Round [124] log likelihood: -85128.370762 EM: Round [125] log likelihood: -85128.370551 EM: Round [126] log likelihood: -85128.370344 EM: Round [127] log likelihood: -85128.370141 EM: Round [128] log likelihood: -85128.369942 EM: Round [129] log likelihood: -85128.369748 EM: Round [130] log likelihood: -85128.369557 EM: Round [131] log likelihood: -85128.369369 EM: Round [132] log likelihood: -85128.369186 EM: Round [133] log likelihood: -85128.369005 EM: Round [134] log likelihood: -85128.368828 EM: Round [135] log likelihood: -85128.368654 EM: Round [136] log likelihood: -85128.368484 EM: Round [137] log likelihood: -85128.368316 EM: Round [138] log likelihood: -85128.368151 EM: Round [139] log likelihood: -85128.367990 EM: Round [140] log likelihood: -85128.367831 EM: Round [141] log likelihood: -85128.367675 EM: Round [142] log likelihood: -85128.367521 EM: Round [143] log likelihood: -85128.367370 EM: Round [144] log likelihood: -85128.367222 EM: Round [145] log likelihood: -85128.367076 EM: Round [146] log likelihood: -85128.366933 EM: Round [147] log likelihood: -85128.366791 EM: Round [148] log likelihood: -85128.366653 EM: Round [149] log likelihood: -85128.366516 EM: Round [150] log likelihood: -85128.366382 EM: Round [151] log likelihood: -85128.366250 EM: Round [152] log likelihood: -85128.366120 EM: Round [153] log likelihood: -85128.365992 EM: Round [154] log likelihood: -85128.365866 EM: Round [155] log likelihood: -85128.365743 EM: Round [156] log likelihood: -85128.365621 EM: Round [157] log likelihood: -85128.365501 EM: Round [158] log likelihood: -85128.365383 EM: Round [159] log likelihood: -85128.365267 EM: Round [160] log likelihood: -85128.365152 EM: Round [161] log likelihood: -85128.365040 EM: Round [162] log likelihood: -85128.364929 EM: Round [163] log likelihood: -85128.364820 EM: Round [164] log likelihood: -85128.364712 EM: Round [165] log likelihood: -85128.364606 EM: Round [166] log likelihood: -85128.364502 EM: Round [167] log likelihood: -85128.364399 EM: Round [168] log likelihood: -85128.364298 EM: Round [169] log likelihood: -85128.364199 EM: Stopping iterations at round 169 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.sFcDrj6eoQ/./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.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.sFcDrj6eoQ/./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.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 67574114 > /tmp/nxf.sFcDrj6eoQ/./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.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir > /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir --annotate /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.sFcDrj6eoQ/./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.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir -done, see /tmp/nxf.sFcDrj6eoQ/./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.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.sFcDrj6eoQ/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 323, filtered: 3932) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.sFcDrj6eoQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.sFcDrj6eoQ/./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.sFcDrj6eoQ/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000229739.4] WARNING, no entry stored in dbm for [ENSG00000234996.4] WARNING, no entry stored in dbm for [ENSG00000277283.1] WARNING, no entry stored in dbm for [ENSG00000225292.2] WARNING, no entry stored in dbm for [ENSG00000228327.3] WARNING, no entry stored in dbm for [ENSG00000248323.7] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000229807.12] WARNING, no entry stored in dbm for [ENSG00000225465.10] WARNING, no entry stored in dbm for [ENSG00000197251.3] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000203865.11] WARNING, no entry stored in dbm for [ENSG00000227220.1] WARNING, no entry stored in dbm for [ENSG00000282375.1] WARNING, no entry stored in dbm for [ENSG00000228998.4] WARNING, no entry stored in dbm for [ENSG00000257167.2] WARNING, no entry stored in dbm for [ENSG00000185986.12] WARNING, no entry stored in dbm for [ENSG00000264911.1] WARNING, no entry stored in dbm for [ENSG00000178107.2] WARNING, no entry stored in dbm for [ENSG00000267248.3] WARNING, no entry stored in dbm for [ENSG00000266179.2] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000241656.1] WARNING, no entry stored in dbm for [ENSG00000223974.1] WARNING, no entry stored in dbm for [ENSG00000232894.1] WARNING, no entry stored in dbm for [ENSG00000249072.1] WARNING, no entry stored in dbm for [ENSG00000223768.2] WARNING, no entry stored in dbm for [ENSG00000241316.8] WARNING, no entry stored in dbm for [ENSG00000203262.3] WARNING, no entry stored in dbm for [ENSG00000248890.2] WARNING, no entry stored in dbm for [ENSG00000199753.1] WARNING, no entry stored in dbm for [ENSG00000262202.4] WARNING, no entry stored in dbm for [ENSG00000199753.1] WARNING, no entry stored in dbm for [ENSG00000262202.4] WARNING, no entry stored in dbm for [ENSG00000255153.1] WARNING, no entry stored in dbm for [ENSG00000240241.5] WARNING, no entry stored in dbm for [ENSG00000223396.4] WARNING, no entry stored in dbm for [ENSG00000226407.1] WARNING, no entry stored in dbm for [ENSG00000206975.1] WARNING, no entry stored in dbm for [ENSG00000251889.1] WARNING, no entry stored in dbm for [ENSG00000201648.1] WARNING, no entry stored in dbm for [ENSG00000251889.1] WARNING, no entry stored in dbm for [ENSG00000201806.1] WARNING, no entry stored in dbm for [ENSG00000180846.8] WARNING, no entry stored in dbm for [ENSG00000201793.1] WARNING, no entry stored in dbm for [ENSG00000199719.1] WARNING, no entry stored in dbm for [ENSG00000201793.1] WARNING, no entry stored in dbm for [ENSG00000201564.1] WARNING, no entry stored in dbm for [ENSG00000201793.1] WARNING, no entry stored in dbm for [ENSG00000223056.1] 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 [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000200794.1] WARNING, no entry stored in dbm for [ENSG00000201428.1] WARNING, no entry stored in dbm for [ENSG00000201564.1] WARNING, no entry stored in dbm for [ENSG00000201428.1] WARNING, no entry stored in dbm for [ENSG00000223056.1] WARNING, no entry stored in dbm for [ENSG00000200379.1] WARNING, no entry stored in dbm for [ENSG00000201758.1] WARNING, no entry stored in dbm for [ENSG00000200379.1] WARNING, no entry stored in dbm for [ENSG00000200673.1] WARNING, no entry stored in dbm for [ENSG00000201794.1] WARNING, no entry stored in dbm for [ENSG00000200131.1] WARNING, no entry stored in dbm for [ENSG00000201600.1] WARNING, no entry stored in dbm for [ENSG00000199719.1] WARNING, no entry stored in dbm for [ENSG00000201600.1] WARNING, no entry stored in dbm for [ENSG00000201564.1] WARNING, no entry stored in dbm for [ENSG00000201600.1] WARNING, no entry stored in dbm for [ENSG00000223056.1] WARNING, no entry stored in dbm for [ENSG00000270938.1] WARNING, no entry stored in dbm for [ENSG00000241570.8] WARNING, no entry stored in dbm for [ENSG00000259856.1] WARNING, no entry stored in dbm for [ENSG00000274356.1] WARNING, no entry stored in dbm for [ENSG00000080947.15] WARNING, no entry stored in dbm for [ENSG00000249419.1] WARNING, no entry stored in dbm for [ENSG00000281903.2] WARNING, no entry stored in dbm for [ENSG00000237187.9] WARNING, no entry stored in dbm for [ENSG00000248360.7] WARNING, no entry stored in dbm for [ENSG00000270231.4] WARNING, no entry stored in dbm for [ENSG00000233321.2] WARNING, no entry stored in dbm for [ENSG00000287624.1] WARNING, no entry stored in dbm for [ENSG00000242324.1] WARNING, no entry stored in dbm for [ENSG00000287754.1] WARNING, no entry stored in dbm for [ENSG00000286807.1] WARNING, no entry stored in dbm for [ENSG00000229891.2] WARNING, no entry stored in dbm for [ENSG00000232903.2] WARNING, no entry stored in dbm for [ENSG00000232677.9] WARNING, no entry stored in dbm for [ENSG00000268163.1] WARNING, no entry stored in dbm for [ENSG00000260807.7] WARNING, no entry stored in dbm for [ENSG00000226145.7] WARNING, no entry stored in dbm for [ENSG00000283103.3] WARNING, no entry stored in dbm for [ENSG00000286694.1] WARNING, no entry stored in dbm for [ENSG00000285219.2] WARNING, no entry stored in dbm for [ENSG00000248873.1] WARNING, no entry stored in dbm for [ENSG00000237390.1] WARNING, no entry stored in dbm for [ENSG00000229249.7] WARNING, no entry stored in dbm for [ENSG00000214433.4] WARNING, no entry stored in dbm for [ENSG00000166104.15] WARNING, no entry stored in dbm for [ENSG00000166104.15] WARNING, no entry stored in dbm for [ENSG00000231367.6] WARNING, no entry stored in dbm for [ENSG00000277737.3] WARNING, no entry stored in dbm for [ENSG00000237238.3] WARNING, no entry stored in dbm for [ENSG00000283036.3] WARNING, no entry stored in dbm for [ENSG00000270171.1] WARNING, no entry stored in dbm for [ENSG00000229109.2] WARNING, no entry stored in dbm for [ENSG00000196366.3] WARNING, no entry stored in dbm for [ENSG00000234241.1] WARNING, no entry stored in dbm for [ENSG00000242324.1] WARNING, no entry stored in dbm for [ENSG00000237773.7] WARNING, no entry stored in dbm for [ENSG00000280828.1] WARNING, no entry stored in dbm for [ENSG00000236830.7] WARNING, no entry stored in dbm for [ENSG00000286837.1] WARNING, no entry stored in dbm for [ENSG00000231764.10] WARNING, no entry stored in dbm for [ENSG00000231140.3] WARNING, no entry stored in dbm for [ENSG00000204959.4] WARNING, no entry stored in dbm for [ENSG00000278217.1] WARNING, no entry stored in dbm for [ENSG00000287356.1] WARNING, no entry stored in dbm for [ENSG00000258858.1] WARNING, no entry stored in dbm for [ENSG00000285887.1] WARNING, no entry stored in dbm for [ENSG00000235749.3] WARNING, no entry stored in dbm for [ENSG00000232599.1] WARNING, no entry stored in dbm for [ENSG00000288068.1] WARNING, no entry stored in dbm for [ENSG00000226482.1] WARNING, no entry stored in dbm for [ENSG00000285062.1] WARNING, no entry stored in dbm for [ENSG00000278212.2] WARNING, no entry stored in dbm for [ENSG00000270960.1] WARNING, no entry stored in dbm for [ENSG00000251314.2] WARNING, no entry stored in dbm for [ENSG00000276538.1] WARNING, no entry stored in dbm for [ENSG00000224016.2] WARNING, no entry stored in dbm for [ENSG00000273805.1] WARNING, no entry stored in dbm for [ENSG00000273805.1] WARNING, no entry stored in dbm for [ENSG00000266208.1] WARNING, no entry stored in dbm for [ENSG00000205682.2] WARNING, no entry stored in dbm for [ENSG00000267011.5] WARNING, no entry stored in dbm for [ENSG00000237036.5] WARNING, no entry stored in dbm for [ENSG00000271394.1] WARNING, no entry stored in dbm for [ENSG00000200794.1] * STAR-Fusion complete. See output: /tmp/nxf.sFcDrj6eoQ/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)