Yves-CHEN / DENTIST

DENTIST (Detecting Errors iN analyses of summary staTISTics) is a QC tool for summary-data-based analyses.
GNU Lesser General Public License v3.0
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Error: dividing Zero #9

Closed eldronzhou closed 3 years ago

eldronzhou commented 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
eldronzhou commented 3 years ago

It is fixed after adding --with-NA-geno flag. Sorry for bothering you.