Unknown option: input FLAG: 1 refSeqFile = /Volumes/web/spartina/project-oyster-oa/data/Cg-roslin/cgigas_uk_roslin_v1_genomic-mito.fa. bamFileName = zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe.deduplicated.sorted.bam. snpFileName = zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe.SNP-candidates.txt. methCgFileName = zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe.CpG-meth-info.tab. methChgFileName = zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe.CHG-meth-info.tab. methChhFileName = zr3644_19_R1_val_1_val_1_val_1_bismark_bt2_pe.CHH-meth-info.tab. vQualMin = 15. nLayerMax = 1000. vSnpRate = 0.100000. vSnpPerBase = 0.020000. mapqThr = 20. Init chrome name-len array completed, total 647905321 bp of 237 chromosomes. 237 chromes loaded. Init chrome name-idx hash table completed. Init chrome seq array completed. Meth process begins... Chrome updated to NC_047559.1! 500000 records have been dealed. 1000000 records have been dealed. 1500000 records have been dealed. 2000000 records have been dealed. 2500000 records have been dealed. 3000000 records have been dealed. 3500000 records have been dealed. Chrome updated to NC_047560.1! 4000000 records have been dealed. 4500000 records have been dealed. 5000000 records have been dealed. 5500000 records have been dealed. Chrome updated to NC_047561.1! 6000000 records have been dealed. 6500000 records have been dealed. 7000000 records have been dealed. 7500000 records have been dealed. 8000000 records have been dealed. 8500000 records have been dealed. 9000000 records have been dealed. 9500000 records have been dealed. Chrome updated to NC_047562.1! 10000000 records have been dealed. 10500000 records have been dealed. 11000000 records have been dealed. 11500000 records have been dealed. 12000000 records have been dealed. 12500000 records have been dealed. Chrome updated to NC_047563.1! 13000000 records have been dealed. 13500000 records have been dealed. 14000000 records have been dealed. 14500000 records have been dealed. 15000000 records have been dealed. Chrome updated to NC_047564.1! 15500000 records have been dealed. 16000000 records have been dealed. 16500000 records have been dealed. 17000000 records have been dealed. 17500000 records have been dealed. 18000000 records have been dealed. 18500000 records have been dealed. 19000000 records have been dealed. 19500000 records have been dealed. Chrome updated to NC_047565.1! 20000000 records have been dealed. 20500000 records have been dealed. 21000000 records have been dealed. 21500000 records have been dealed. 22000000 records have been dealed. 22500000 records have been dealed. 23000000 records have been dealed. 23500000 records have been dealed. 24000000 records have been dealed. Chrome updated to NC_047566.1! 24500000 records have been dealed. 25000000 records have been dealed. 25500000 records have been dealed. 26000000 records have been dealed. 26500000 records have been dealed. Chrome updated to NC_047567.1! 27000000 records have been dealed. 27500000 records have been dealed. 28000000 records have been dealed. 28500000 records have been dealed. Chrome updated to NC_047568.1! 29000000 records have been dealed. 29500000 records have been dealed. 30000000 records have been dealed. 30500000 records have been dealed. 31000000 records have been dealed. 31500000 records have been dealed. 32000000 records have been dealed. 32500000 records have been dealed. Chrome updated to NW_022994773.1! Chrome updated to NW_022994774.1! Chrome updated to NW_022994775.1! Chrome updated to NW_022994776.1! Chrome updated to NW_022994777.1! Chrome updated to NW_022994778.1! Chrome updated to NW_022994779.1! Chrome updated to NW_022994780.1! Chrome updated to NW_022994781.1! Chrome updated to NW_022994782.1! Chrome updated to NW_022994783.1! Chrome updated to NW_022994784.1! Chrome updated to NW_022994785.1! Chrome updated to NW_022994786.1! Chrome updated to NW_022994787.1! Chrome updated to NW_022994788.1! Chrome updated to NW_022994789.1! Chrome updated to NW_022994790.1! Chrome updated to NW_022994791.1! Chrome updated to NW_022994792.1! Chrome updated to NW_022994793.1! Chrome updated to NW_022994794.1! Chrome updated to NW_022994795.1! Chrome updated to NW_022994796.1! Chrome updated to NW_022994797.1! Chrome updated to NW_022994798.1! Chrome updated to NW_022994799.1! Chrome updated to NW_022994800.1! Chrome updated to NW_022994801.1! Chrome updated to NW_022994802.1! Chrome updated to NW_022994803.1! Chrome updated to NW_022994804.1! Chrome updated to NW_022994805.1! Chrome updated to NW_022994806.1! Chrome updated to NW_022994807.1! Chrome updated to NW_022994808.1! Chrome updated to NW_022994809.1! Chrome updated to NW_022994810.1! Chrome updated to NW_022994811.1! Chrome updated to NW_022994812.1! Chrome updated to NW_022994813.1! Chrome updated to NW_022994814.1! Chrome updated to NW_022994815.1! Chrome updated to NW_022994816.1! Chrome updated to NW_022994817.1! Chrome updated to NW_022994819.1! Chrome updated to NW_022994820.1! Chrome updated to NW_022994821.1! Chrome updated to NW_022994822.1! Chrome updated to NW_022994823.1! Chrome updated to NW_022994824.1! Chrome updated to NW_022994825.1! Chrome updated to NW_022994826.1! Chrome updated to NW_022994827.1! Chrome updated to NW_022994828.1! Chrome updated to NW_022994829.1! Chrome updated to NW_022994830.1! Chrome updated to NW_022994831.1! Chrome updated to NW_022994832.1! 33000000 records have been dealed. Chrome updated to NW_022994833.1! Chrome updated to NW_022994834.1! Chrome updated to NW_022994835.1! Chrome updated to NW_022994836.1! Chrome updated to NW_022994837.1! Chrome updated to NW_022994838.1! Chrome updated to NW_022994839.1! Chrome updated to NW_022994840.1! Chrome updated to NW_022994841.1! Chrome updated to NW_022994842.1! Chrome updated to NW_022994843.1! Chrome updated to NW_022994844.1! Chrome updated to NW_022994845.1! Chrome updated to NW_022994846.1! Chrome updated to NW_022994847.1! Chrome updated to NW_022994848.1! Chrome updated to NW_022994849.1! Chrome updated to NW_022994850.1! Chrome updated to NW_022994851.1! Chrome updated to NW_022994852.1! Chrome updated to NW_022994853.1! Chrome updated to NW_022994854.1! Chrome updated to NW_022994855.1! Chrome updated to NW_022994856.1! Chrome updated to NW_022994857.1! Chrome updated to NW_022994858.1! Chrome updated to NW_022994859.1! Chrome updated to NW_022994860.1! Chrome updated to NW_022994861.1! Chrome updated to NW_022994862.1! Chrome updated to NW_022994863.1! Chrome updated to NW_022994864.1! Chrome updated to NW_022994865.1! Chrome updated to NW_022994866.1! Chrome updated to NW_022994867.1! Chrome updated to NW_022994868.1! Chrome updated to NW_022994869.1! Chrome updated to NW_022994870.1! Chrome updated to NW_022994871.1! Chrome updated to NW_022994872.1! Chrome updated to NW_022994873.1! Chrome updated to NW_022994874.1! Chrome updated to NW_022994875.1! Chrome updated to NW_022994876.1! Chrome updated to NW_022994877.1! Chrome updated to NW_022994878.1! Chrome updated to NW_022994879.1! Chrome updated to NW_022994880.1! Chrome updated to NW_022994881.1! Chrome updated to NW_022994882.1! Chrome updated to NW_022994883.1! Chrome updated to NW_022994884.1! Chrome updated to NW_022994885.1! Chrome updated to NW_022994886.1! Chrome updated to NW_022994887.1! Chrome updated to NW_022994888.1! Chrome updated to NW_022994889.1! Chrome updated to NW_022994890.1! Chrome updated to NW_022994891.1! Chrome updated to NW_022994892.1! Chrome updated to NW_022994893.1! Chrome updated to NW_022994894.1! Chrome updated to NW_022994895.1! Chrome updated to NW_022994896.1! Chrome updated to NW_022994897.1! Chrome updated to NW_022994898.1! Chrome updated to NW_022994899.1! Chrome updated to NW_022994900.1! Chrome updated to NW_022994901.1! Chrome updated to NW_022994902.1! Chrome updated to NW_022994903.1! Chrome updated to NW_022994904.1! Chrome updated to NW_022994905.1! Chrome updated to NW_022994906.1! Chrome updated to NW_022994907.1! Chrome updated to NW_022994908.1! Chrome updated to NW_022994909.1! Chrome updated to NW_022994910.1! Chrome updated to NW_022994911.1! Chrome updated to NW_022994912.1! Chrome updated to NW_022994913.1! Chrome updated to NW_022994914.1! Chrome updated to NW_022994915.1! Chrome updated to NW_022994916.1! Chrome updated to NW_022994917.1! 33500000 records have been dealed. Chrome updated to NW_022994918.1! Chrome updated to NW_022994919.1! Chrome updated to NW_022994920.1! Chrome updated to NW_022994921.1! Chrome updated to NW_022994922.1! Chrome updated to NW_022994923.1! Chrome updated to NW_022994924.1! Chrome updated to NW_022994925.1! Chrome updated to NW_022994926.1! Chrome updated to NW_022994927.1! Chrome updated to NW_022994928.1! Chrome updated to NW_022994929.1! Chrome updated to NW_022994930.1! Chrome updated to NW_022994931.1! Chrome updated to NW_022994932.1! Chrome updated to NW_022994933.1! Chrome updated to NW_022994934.1! Chrome updated to NW_022994935.1! Chrome updated to NW_022994936.1! Chrome updated to NW_022994937.1! Chrome updated to NW_022994938.1! Chrome updated to NW_022994939.1! Chrome updated to NW_022994940.1! Chrome updated to NW_022994941.1! Chrome updated to NW_022994942.1! Chrome updated to NW_022994943.1! Chrome updated to NW_022994944.1! Chrome updated to NW_022994945.1! Chrome updated to NW_022994946.1! Chrome updated to NW_022994947.1! Chrome updated to NW_022994948.1! Chrome updated to NW_022994949.1! Chrome updated to NW_022994950.1! Chrome updated to NW_022994951.1! Chrome updated to NW_022994952.1! Chrome updated to NW_022994953.1! Chrome updated to NW_022994954.1! Chrome updated to NW_022994955.1! Chrome updated to NW_022994956.1! Chrome updated to NW_022994957.1! Chrome updated to NW_022994958.1! Chrome updated to NW_022994959.1! Chrome updated to NW_022994960.1! 34000000 records have been dealed. Chrome updated to NW_022994961.1! Chrome updated to NW_022994962.1! Chrome updated to NW_022994963.1! Chrome updated to NW_022994964.1! Chrome updated to NW_022994965.1! Chrome updated to NW_022994966.1! Chrome updated to NW_022994967.1! Chrome updated to NW_022994968.1! Chrome updated to NW_022994969.1! Chrome updated to NW_022994970.1! Chrome updated to NW_022994971.1! Chrome updated to NW_022994972.1! Chrome updated to NW_022994973.1! Chrome updated to NW_022994974.1! Chrome updated to NW_022994975.1! Chrome updated to NW_022994976.1! Chrome updated to NW_022994977.1! Chrome updated to NW_022994978.1! Chrome updated to NW_022994979.1! Chrome updated to NW_022994980.1! Chrome updated to NW_022994981.1! Chrome updated to NW_022994982.1! Chrome updated to NW_022994983.1! Chrome updated to NW_022994984.1! Chrome updated to NW_022994985.1! Chrome updated to NW_022994986.1! Chrome updated to NW_022994987.1! Chrome updated to NW_022994988.1! Chrome updated to NW_022994989.1! Chrome updated to NW_022994990.1! Chrome updated to NW_022994991.1! Chrome updated to NW_022994992.1! Chrome updated to NW_022994993.1! Chrome updated to NW_022994994.1! Chrome updated to NW_022994995.1! Chrome updated to NW_022994996.1! Chrome updated to NW_022994997.1! Chrome updated to NW_022994998.1! Chrome updated to NC_001276.1! Meth process ends... SNP process begins... 100000 records have been dealed. 200000 records have been dealed. 300000 records have been dealed. 400000 records have been dealed. 500000 records have been dealed. 600000 records have been dealed. 700000 records have been dealed. 800000 records have been dealed. 900000 records have been dealed. 1000000 records have been dealed. 1100000 records have been dealed. 1200000 records have been dealed. 1300000 records have been dealed. 1400000 records have been dealed. 1500000 records have been dealed. 1600000 records have been dealed. 1700000 records have been dealed. 1800000 records have been dealed. 1900000 records have been dealed. 2000000 records have been dealed. 2100000 records have been dealed. 2200000 records have been dealed. 2300000 records have been dealed. 2400000 records have been dealed. 2500000 records have been dealed. 2600000 records have been dealed. 2700000 records have been dealed. 2800000 records have been dealed. 2900000 records have been dealed. 3000000 records have been dealed. 3100000 records have been dealed. 3200000 records have been dealed. 3300000 records have been dealed. 3400000 records have been dealed. 3500000 records have been dealed. 3600000 records have been dealed. 3700000 records have been dealed. 3800000 records have been dealed. 3900000 records have been dealed. 4000000 records have been dealed. 4100000 records have been dealed. 4200000 records have been dealed. 4300000 records have been dealed. 4400000 records have been dealed. 4500000 records have been dealed. 4600000 records have been dealed. 4700000 records have been dealed. 4800000 records have been dealed. 4900000 records have been dealed. 5000000 records have been dealed. 5100000 records have been dealed. 5200000 records have been dealed. 5300000 records have been dealed. 5400000 records have been dealed. 5500000 records have been dealed. 5600000 records have been dealed. 5700000 records have been dealed. 5800000 records have been dealed. 5900000 records have been dealed. 6000000 records have been dealed. 6100000 records have been dealed. 6200000 records have been dealed. 6300000 records have been dealed. 6400000 records have been dealed. 6500000 records have been dealed. 6600000 records have been dealed. 6700000 records have been dealed. 6800000 records have been dealed. 6900000 records have been dealed. 7000000 records have been dealed. 7100000 records have been dealed. 7200000 records have been dealed. 7300000 records have been dealed. 7400000 records have been dealed. 7500000 records have been dealed. 7600000 records have been dealed. 7700000 records have been dealed. 7800000 records have been dealed. 7900000 records have been dealed. 8000000 records have been dealed. 8100000 records have been dealed. 8200000 records have been dealed. 8300000 records have been dealed. 8400000 records have been dealed. 8500000 records have been dealed. 8600000 records have been dealed. 8700000 records have been dealed. 8800000 records have been dealed. 8900000 records have been dealed. 9000000 records have been dealed. 9100000 records have been dealed. 9200000 records have been dealed. 9300000 records have been dealed. 9400000 records have been dealed. 9500000 records have been dealed. 9600000 records have been dealed. 9700000 records have been dealed. 9800000 records have been dealed. 9900000 records have been dealed. 10000000 records have been dealed. 10100000 records have been dealed. 10200000 records have been dealed. 10300000 records have been dealed. 10400000 records have been dealed. 10500000 records have been dealed. 10600000 records have been dealed. 10700000 records have been dealed. 10800000 records have been dealed. 10900000 records have been dealed. 11000000 records have been dealed. 11100000 records have been dealed. 11200000 records have been dealed. 11300000 records have been dealed. 11400000 records have been dealed. 11500000 records have been dealed. 11600000 records have been dealed. 11700000 records have been dealed. 11800000 records have been dealed. 11900000 records have been dealed. 12000000 records have been dealed. 12100000 records have been dealed. 12200000 records have been dealed. 12300000 records have been dealed. 12400000 records have been dealed. 12500000 records have been dealed. 12600000 records have been dealed. 12700000 records have been dealed. 12800000 records have been dealed. 12900000 records have been dealed. 13000000 records have been dealed. 13100000 records have been dealed. 13200000 records have been dealed. 13300000 records have been dealed. 13400000 records have been dealed. 13500000 records have been dealed. 13600000 records have been dealed. 13700000 records have been dealed. 13800000 records have been dealed. 13900000 records have been dealed. 14000000 records have been dealed. 14100000 records have been dealed. 14200000 records have been dealed. 14300000 records have been dealed. 14400000 records have been dealed. 14500000 records have been dealed. 14600000 records have been dealed. 14700000 records have been dealed. 14800000 records have been dealed. 14900000 records have been dealed. 15000000 records have been dealed. 15100000 records have been dealed. 15200000 records have been dealed. 15300000 records have been dealed. 15400000 records have been dealed. 15500000 records have been dealed. 15600000 records have been dealed. 15700000 records have been dealed. 15800000 records have been dealed. 15900000 records have been dealed. 16000000 records have been dealed. 16100000 records have been dealed. 16200000 records have been dealed. 16300000 records have been dealed. 16400000 records have been dealed. 16500000 records have been dealed. 16600000 records have been dealed. 16700000 records have been dealed. 16800000 records have been dealed. 16900000 records have been dealed. 17000000 records have been dealed. 17100000 records have been dealed. 17200000 records have been dealed. 17300000 records have been dealed. 17400000 records have been dealed. 17500000 records have been dealed. 17600000 records have been dealed. 17700000 records have been dealed. 17800000 records have been dealed. 17900000 records have been dealed. 18000000 records have been dealed. 18100000 records have been dealed. 18200000 records have been dealed. 18300000 records have been dealed. 18400000 records have been dealed. 18500000 records have been dealed. 18600000 records have been dealed. 18700000 records have been dealed. 18800000 records have been dealed. 18900000 records have been dealed. 19000000 records have been dealed. 19100000 records have been dealed. 19200000 records have been dealed. 19300000 records have been dealed. 19400000 records have been dealed. 19500000 records have been dealed. 19600000 records have been dealed. 19700000 records have been dealed. 19800000 records have been dealed. 19900000 records have been dealed. 20000000 records have been dealed. 20100000 records have been dealed. 20200000 records have been dealed. 20300000 records have been dealed. 20400000 records have been dealed. 20500000 records have been dealed. 20600000 records have been dealed. 20700000 records have been dealed. 20800000 records have been dealed. 20900000 records have been dealed. 21000000 records have been dealed. 21100000 records have been dealed. 21200000 records have been dealed. 21300000 records have been dealed. 21400000 records have been dealed. 21500000 records have been dealed. 21600000 records have been dealed. 21700000 records have been dealed. 21800000 records have been dealed. 21900000 records have been dealed. 22000000 records have been dealed. 22100000 records have been dealed. 22200000 records have been dealed. 22300000 records have been dealed. 22400000 records have been dealed. 22500000 records have been dealed. 22600000 records have been dealed. 22700000 records have been dealed. 22800000 records have been dealed. 22900000 records have been dealed. 23000000 records have been dealed. 23100000 records have been dealed. 23200000 records have been dealed. 23300000 records have been dealed. 23400000 records have been dealed. 23500000 records have been dealed. 23600000 records have been dealed. 23700000 records have been dealed. 23800000 records have been dealed. 23900000 records have been dealed. 24000000 records have been dealed. 24100000 records have been dealed. 24200000 records have been dealed. 24300000 records have been dealed. 24400000 records have been dealed. 24500000 records have been dealed. 24600000 records have been dealed. 24700000 records have been dealed. 24800000 records have been dealed. 24900000 records have been dealed. 25000000 records have been dealed. 25100000 records have been dealed. 25200000 records have been dealed. 25300000 records have been dealed. 25400000 records have been dealed. 25500000 records have been dealed. 25600000 records have been dealed. 25700000 records have been dealed. 25800000 records have been dealed. 25900000 records have been dealed. 26000000 records have been dealed. 26100000 records have been dealed. 26200000 records have been dealed. 26300000 records have been dealed. 26400000 records have been dealed. 26500000 records have been dealed. 26600000 records have been dealed. 26700000 records have been dealed. 26800000 records have been dealed. 26900000 records have been dealed. 27000000 records have been dealed. 27100000 records have been dealed. 27200000 records have been dealed. 27300000 records have been dealed. 27400000 records have been dealed. 27500000 records have been dealed. 27600000 records have been dealed. 27700000 records have been dealed. 27800000 records have been dealed. 27900000 records have been dealed. 28000000 records have been dealed. 28100000 records have been dealed. 28200000 records have been dealed. 28300000 records have been dealed. 28400000 records have been dealed. 28500000 records have been dealed. 28600000 records have been dealed. 28700000 records have been dealed. 28800000 records have been dealed. 28900000 records have been dealed. 29000000 records have been dealed. 29100000 records have been dealed. 29200000 records have been dealed. 29300000 records have been dealed. 29400000 records have been dealed. 29500000 records have been dealed. 29600000 records have been dealed. 29700000 records have been dealed. 29800000 records have been dealed. 29900000 records have been dealed. 30000000 records have been dealed. 30100000 records have been dealed. 30200000 records have been dealed. 30300000 records have been dealed. 30400000 records have been dealed. 30500000 records have been dealed. 30600000 records have been dealed. 30700000 records have been dealed. 30800000 records have been dealed. 30900000 records have been dealed. 31000000 records have been dealed. 31100000 records have been dealed. 31200000 records have been dealed. 31300000 records have been dealed. 31400000 records have been dealed. 31500000 records have been dealed. 31600000 records have been dealed. 31700000 records have been dealed. 31800000 records have been dealed. 31900000 records have been dealed. 32000000 records have been dealed. 32100000 records have been dealed. 32200000 records have been dealed. 32300000 records have been dealed. 32400000 records have been dealed. 32500000 records have been dealed. 32600000 records have been dealed. 32700000 records have been dealed. 32800000 records have been dealed. 32900000 records have been dealed. 33000000 records have been dealed. 33100000 records have been dealed. 33200000 records have been dealed. 33300000 records have been dealed. 33400000 records have been dealed. 33500000 records have been dealed. 33600000 records have been dealed. 33700000 records have been dealed. 33800000 records have been dealed. 33900000 records have been dealed. 34000000 records have been dealed. 34100000 records have been dealed. 34200000 records have been dealed. 34300000 records have been dealed. 34400000 records have been dealed. SNP process ends... SNP process completed.