Closed eldronzhou closed 3 years ago
Hi,
I encountered following dividing zero error when running DENTIST on my data.
[gz222@p02r09n24 10K]$ DENTIST --gwas-summary sim_1_cojo.txt --bfile /ysm-gpfs/pi/zhao/gz222/UKB_simulate/genotype/validate/validate_10K --chrID 1
******************************************************************* * DENTIST (Detecting Errors iN analyses of summary staTISTics) * Version 0.9.2.1 * (C) 2018 Wenhan Chen, Zhihong Zhu and Jian Yang * The University of Queensland * MIT License ******************************************************************* --gwas-summary sim_1_cojo.txt --bfile /ysm-gpfs/pi/zhao/gz222/UKB_simulate/genotype/validate/validate_10K --chrID 1 Reading GWAS summary data from [sim_1_cojo.txt]. Reserving 1 M memory for reading. GWAS summary data of 681828 SNPs to be included from [sim_1_cojo.txt]. [warning] mogan is like to be missing, but it will only be a problem when calling for it. [info] Calculating frequencies with 1 cpus [info] This bed file is plink 1.0 bedfile format. (Older) [info] chrID == 1 [info] Aligning GWAS to the reference sample assumming both files are ordered. [info] Performing DENTIST at 681828 SNPs shared between the summary and reference data. 0-319, 1960761, 0 112-544, 1960753, 0 318-827, 1983044, 0 543-1153, 1984723, 0 826-1416, 1993769, 0 1152-1648, 1989820, 0 1415-1845, 1989708, 0 1647-2038, 1992972, 0 1844-2268, 1993346, 0 2037-2432, 1988573, 0 2267-2677, 1990580, 0 2431-2740, 1510888, 0 2740-3340, 1979458, 0 3070-3640, 1982795, 0 3339-3854, 1953314, 0 3639-4132, 1957114, 0 3853-4423, 1985330, 0 4131-4741, 1990136, 0 4422-4979, 1985472, 0 4740-5249, 1987085, 0 4978-5487, 1962063, 0 5248-5696, 1946431, 0 5486-5944, 1929418, 0 5695-6204, 1947364, 0 5943-6436, 1997105, 0 6203-6578, 1987261, 0 6435-6809, 1966415, 0 6577-6974, 1814639, 0 6808-7275, 1820476, 0 6973-7549, 1978641, 0 7274-7670, 1974088, 0 7548-7936, 1973531, 0 7669-8229, 1993077, 0 7935-8277, 1970973, 0 8228-8480, 1966695, 0 8276-8754, 1986777, 0 8479-8999, 1960776, 0 8753-9230, 1966754, 0 8998-9514, 1991806, 0 9229-9775, 1985344, 0 9513-10005, 1983471, 0 9774-10309, 1987190, 0 10004-10555, 1989925, 0 10308-10795, 1983008, 0 10554-11033, 1957317, 0 10794-11314, 1953075, 0 11032-11576, 1977710, 0 11313-11740, 1986383, 0 11575-11894, 1961225, 0 11739-12028, 1955839, 0 11893-12154, 1964245, 0 12027-12394, 1964693, 0 12153-12649, 1976220, 0 12393-12963, 1964902, 0 12648-13283, 1964663, 0 12962-13638, 1969222, 0 13282-13984, 1972533, 0 13637-14250, 1983282, 0 13983-14507, 1974439, 0 14249-14760, 1961904, 0 14506-15014, 1969365, 0 14759-15263, 1974299, 0 15013-15534, 1970823, 0 15262-15798, 1982099, 0 15533-16076, 1984996, 0 15797-16459, 1977433, 0 16075-16731, 1985652, 0 16458-16923, 1979197, 0 16730-17156, 1958738, 0 16922-17417, 1975550, 0 17155-17584, 1994331, 0 17416-17747, 1994748, 0 17583-17978, 1996765, 0 17746-18240, 1986243, 0 17977-18542, 1978121, 0 18239-18844, 1984767, 0 18541-19092, 1980865, 0 18843-19317, 1959266, 0 19091-19544, 1967438, 0 19316-19797, 1990708, 0 19543-20137, 1995239, 0 19796-20437, 1994765, 0 20136-20692, 1991110, 0 20436-20995, 1992716, 0 20691-21332, 1992041, 0 20994-21578, 1989591, 0 21331-21801, 1990404, 0 21577-22016, 1978418, 0 21800-22258, 1961579, 0 22015-22510, 1968992, 0 22257-22836, 1986787, 0 22509-23050, 1990363, 0 22835-23321, 1979918, 0 23049-23561, 1982486, 0 23320-23850, 1994127, 0 23560-24130, 1991988, 0 23849-24425, 1957886, 0 24129-24705, 1951304, 0 24424-24968, 1986294, 0 24704-25249, 1997147, 0 24967-25566, 1994561, 0 25248-25818, 1969257, 0 25565-25918, 1957201, 0 25817-26148, 1979370, 0 25917-26360, 1991860, 0 26147-26610, 1983918, 0 26359-26879, 1980899, 0 26609-27085, 1891522, 0 26878-27343, 1880819, 0 27084-27635, 1963914, 0 27342-28024, 1979268, 0 27634-28303, 1979285, 0 28023-28546, 1977550, 0 28302-28808, 1984996, 0 28545-29096, 1987909, 0 28807-29265, 1976194, 0 29095-29530, 1941722, 0 29264-29770, 1921900, 0 29529-30016, 1953330, 0 29625-30101, 1777862, 0 30103-30104, 0, 0 30107-30177, 334720, 0 30398-30500, 821847, 0 30500-30919, 1980310, 0 30695-31210, 1986082, 0 30918-31525, 1988577, 0 31209-31788, 1996599, 0 31524-31967, 1987396, 0 31787-32219, 1985311, 0 31966-32524, 1959743, 0 32218-32840, 1961049, 0 32523-33111, 1980178, 0 32839-33385, 1982567, 0 33110-33612, 1997062, 0 33384-33950, 1984704, 0 33611-34296, 1985354, 0 33949-34582, 1997348, 0 34295-34934, 1989409, 0 34581-35257, 1984804, 0 34933-35605, 1988799, 0 35256-35886, 1986072, 0 35604-36306, 1988644, 0 35885-36633, 1991675, 0 36305-37028, 1992621, 0 36632-37385, 1996635, 0 37027-37576, 1977529, 0 37384-37825, 1978195, 0 37575-38145, 1988437, 0 37824-38388, 1980286, 0 38144-38640, 1912370, 0 38387-38897, 1920930, 0 38639-39279, 1994330, 0 38896-39578, 1990197, 0 39278-39872, 1989095, 0 39577-40171, 1989535, 0 39871-40434, 1992712, 0 40170-40754, 1984164, 0 40433-40996, 1959199, 0 40753-41203, 1946076, 0 40995-41462, 1967789, 0 41202-41816, 1992656, 0 41461-42010, 1919338, 0 41815-42279, 1915269, 0 42009-42570, 1983812, 0 42278-42789, 1984097, 0 42569-43028, 1981450, 0 42788-43275, 1973033, 0 43027-43564, 1967748, 0 43274-43821, 1928200, 0 43563-44002, 1945019, 0 43820-44249, 1991810, 0 44001-44470, 1966112, 0 44248-44752, 1923612, 0 44469-45078, 1948222, 0 44751-45441, 1987162, 0 45077-45676, 1984220, 0 45440-45950, 1981763, 0 45675-46298, 1984043, 0 45949-46601, 1839857, 0 46297-46677, 1710211, 0 46600-46921, 1864430, 0 46676-47260, 1991134, 0 46920-47540, 1978798, 0 47259-47874, 1980822, 0 47539-48129, 1985938, 0 47873-48371, 1986703, 0 48128-48636, 1979912, 0 48370-48929, 1983207, 0 48635-49184, 1990187, 0 48928-49469, 1989635, 0 49183-49851, 1983546, 0 49468-50111, 1973913, 0 49850-50425, 1983964, 0 50110-50700, 1990480, 0 50424-50923, 1993785, 0 50699-51133, 1953619, 0 50922-51335, 1947048, 0 51132-51521, 1937047, 0 51334-51750, 1940408, 0 51520-51955, 1989673, 0 51749-52283, 1993251, 0 51954-52569, 1983210, 0 52282-52815, 1960088, 0 52568-53057, 1966012, 0 52814-53391, 1979096, 0 53056-53653, 1980211, 0 53390-54018, 1987828, 0 53652-54309, 1987554, 0 54017-54553, 1984602, 0 54308-54813, 1944442, 0 54552-55178, 1948249, 0 54812-55464, 1960941, 0 55177-55787, 1960429, 0 55463-56058, 1995723, 0 55786-56356, 1998376, 0 56057-56679, 1995784, 0 56355-56916, 1985136, 0 56678-57176, 1979740, 0 56915-57406, 1985377, 0 57175-57749, 1986460, 0 57405-58024, 1990692, 0 57748-58295, 1992944, 0 57892-681828, 4099299607, 0 681826-681828, 4129, 0 681827-681828, 0, 0 681827-681828, 0, 0 681827-681828, 0, 0 681827-681828, 0, 0 681826-681828, 4129, 0 681827-681828, 0, 0 681826-681828, 4129, 0 679639-680190, 1490611, 0 681827-681828, 0, 0 681826-681828, 4129, 0 681506-681828, 1213942, 0 681827-681828, 0, 0 681826-681828, 4129, 0 676813-677400, 1467862, 0 681827-681828, 0, 0 681826-681828, 4129, 0 681827-681828, 0, 0 681827-681828, 0, 0 681826-681828, 4129, 0 679233-679801, 1496638, 0 678160-678522, 1476309, 0 680575-681104, 1494996, 0 681826-681828, 4129, 0 681827-681828, 0, 0 681827-681828, 0, 0 681826-681828, 4129, 0 679116-679662, 1494528, 0 680770-681337, 1494089, 0 681062-681605, 1485041, 0 681459-681828, 1307695, 0 681826-681828, 4129, 0 681827-681828, 0, 0 681826-681828, 4129, 0 679849-680307, 1493812, 0 678140-678508, 1495490, 0 681826-681828, 4129, 0 681826-681828, 4129, 0 681827-681828, 0, 0 681826-681828, 4129, 0 681818-681828, 24276, 0 681731-681828, 345582, 0 680597-681119, 1498688, 0 680320-680759, 1492534, 0 681827-681828, 0, 0 681826-681828, 4129, 0 676976-677476, 1472779, 0 676906-677457, 1477477, 0 680455-680933, 1481713, 0 681826-681828, 4129, 0 676432-676961, 1495794, 0 679967-680369, 1478601, 0 681826-681828, 4129, 0 677922-678310, 1486579, 0 681826-681828, 4129, 0 636916-676979, 6987642, 0 681826-681828, 4129, 0 653175-677729, 7598770, 0 681826-681828, 4129, 0 671876-681539, 33183267, 0 681154-681805, 1987785, 0 681335-681828, 1596485, 0 [info] At least 4096 Mb of memory is required. 112th - 544th ..0.4%[info] LD matrix size is 1 Mb. [error] Divividing zero : Rsq = 1.003666
It is fixed after adding --with-NA-geno flag. Sorry for bothering you.
Hi,
I encountered following dividing zero error when running DENTIST on my data.
[gz222@p02r09n24 10K]$ DENTIST --gwas-summary sim_1_cojo.txt --bfile /ysm-gpfs/pi/zhao/gz222/UKB_simulate/genotype/validate/validate_10K --chrID 1