{"action":"created","issue":{"url":"https://api.github.com/repos/choishingwan/PRSice/issues/88","repository_url":"https://api.github.com/repos/choishingwan/PRSice","labels_url":"https://api.github.com/repos/choishingwan/PRSice/issues/88/labels{/name}","comments_url":"https://api.github.com/repos/choishingwan/PRSice/issues/88/comments","events_url":"https://api.github.com/repos/choishingwan/PRSice/issues/88/events","html_url":"https://github.com/choishingwan/PRSice/issues/88","id":393084497,"node_id":"MDU6SXNzdWUzOTMwODQ0OTc=","number":88,"title":"Error: can not open .bim file","user":{"login":"mehul4frnds","id":40570544,"node_id":"MDQ6VXNlcjQwNTcwNTQ0","avatar_url":"https://avatars3.githubusercontent.com/u/40570544?v=4","gravatar_id":"","url":"https://api.github.com/users/mehul4frnds","html_url":"https://github.com/mehul4frnds","followers_url":"https://api.github.com/users/mehul4frnds/followers","following_url":"https://api.github.com/users/mehul4frnds/following{/other_user}","gists_url":"https://api.github.com/users/mehul4frnds/gists{/gist_id}","starred_url":"https://api.github.com/users/mehul4frnds/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mehul4frnds/subscriptions","organizations_url":"https://api.github.com/users/mehul4frnds/orgs","repos_url":"https://api.github.com/users/mehul4frnds/repos","events_url":"https://api.github.com/users/mehul4frnds/events{/privacy}","received_events_url":"https://api.github.com/users/mehul4frnds/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2018-12-20T15:05:04Z","updated_at":"2018-12-20T16:50:19Z","closed_at":null,"author_association":"NONE","body":"#I used shell script to run the command\r\n#!/bin/sh\r\n\r\n\r\nRscript PRSice.R --dir . \\\r\n    --prsice ./PRSice_linux \\\r\n    --base /home/cnap_lab_gwas/Downloads/try_2.assoc \\\r\n    --target /mnt/data/hrc_plinkb/chr#_MDRF_hrcimputedbed,chr1_MDRF_hrcimputedb$\r\n    --type bed \\\r\n    --out /home/cnap_lab_gwas/mehul_PRS/HDL_mdrf_1912 \\\r\n    --thread 1 \\\r\n    --stat BETA \\\r\n    --beta \\\r\n    --binary-target F\r\n\r\nit displayed the following error:\r\n\r\nPRSice 2.1.4.beta (19 October 2018) \r\nhttps://github.com/choishingwan/PRSice\r\n(C) 2016-2017 Shing Wan (Sam) Choi, Jack Euesden, Cathryn M. Lewis, Paul F. O'Reilly\r\nGNU General Public License v3\r\n\r\nIf you use PRSice in any published work, please cite:\r\nJack Euesden Cathryn M. Lewis Paul F. O'Reilly (2015)\r\nPRSice: Polygenic Risk Score software.\r\nBioinformatics 31 (9): 1466-1468\r\n\r\n2018-12-20 15:03:53\r\n./PRSice_linux \\\r\n    --A1 A1 \\\r\n    --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \\\r\n    --base /home/cnap_lab_gwas/Downloads/try_2.assoc \\\r\n    --beta  \\\r\n    --binary-target F \\\r\n    --bp BP \\\r\n    --chr CHR \\\r\n    --clump-kb 250 \\\r\n    --clump-p 1.000000 \\\r\n    --clump-r2 0.100000 \\\r\n    --interval 5e-05 \\\r\n    --lower 0.0001 \\\r\n    --model add \\\r\n    --out /home/cnap_lab_gwas/mehul_PRS/HDL_mdrf_1912 \\\r\n    --pvalue P \\\r\n    --seed 3694859724 \\\r\n    --snp SNP \\\r\n    --stat BETA \\\r\n    --target /mnt/data/hrc_plinkb/chr#_MDRF_hrcimputedbed,chr1_MDRF_hrcimputedbed.fam \\\r\n    --thread 1 \\\r\n    --type bed \\\r\n    --upper 0.5\r\n\r\n\r\nLoading Genotype file: \r\n/mnt/data/hrc_plinkb/chr#_MDRF_hrcimputedbed,chr1_MDRF_hrcimputedbed.fam \r\n(bed) \r\nWith external fam file: chr1_MDRF_hrcimputedbed.fam \r\n \r\n\r\n2059 people (0 male(s), 0 female(s)) observed \r\n2059 founder(s) included \r\n \r\n\r\n**Error: Cannot open bim file: \r\n       /mnt/data/hrc_plinkb/chr1_MDRF_hrcimputedbed.bim** \r\n\r\nError: \r\nExecution halted\r\n\r\nPlease suggest, how to avoid these problem. \r\nThanks in advance\r\n"},"comment":{"url":"https://api.github.com/repos/choishingwan/PRSice/issues/comments/449063123","html_url":"https://github.com/choishingwan/PRSice/issues/88#issuecomment-449063123","issue_url":"https://api.github.com/repos/choishingwan/PRSice/issues/88","id":449063123,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0OTA2MzEyMw==","user":{"login":"mehul4frnds","id":40570544,"node_id":"MDQ6VXNlcjQwNTcwNTQ0","avatar_url":"https://avatars3.githubusercontent.com/u/40570544?v=4","gravatar_id":"","url":"https://api.github.com/users/mehul4frnds","html_url":"https://github.com/mehul4frnds","followers_url":"https://api.github.com/users/mehul4frnds/followers","following_url":"https://api.github.com/users/mehul4frnds/following{/other_user}","gists_url":"https://api.github.com/users/mehul4frnds/gists{/gist_id}","starred_url":"https://api.github.com/users/mehul4frnds/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mehul4frnds/subscriptions","organizations_url":"https://api.github.com/users/mehul4frnds/orgs","repos_url":"https://api.github.com/users/mehul4frnds/repos","events_url":"https://api.github.com/users/mehul4frnds/events{/privacy}","received_events_url":"https://api.github.com/users/mehul4frnds/received_events","type":"User","site_admin":false},"created_at":"2018-12-20T16:50:19Z","updated_at":"2018-12-20T16:50:19Z","author_association":"NONE","body":"I tried with another method too such as, to keep all the binary files in the same folder, but it shows another error:\r\n\r\nPRSice 2.1.5 (7 November 2018) \r\nhttps://github.com/choishingwan/PRSice\r\n(C) 2016-2017 Shing Wan (Sam) Choi, Jack Euesden, Cathryn M. Lewis, Paul F. O'Reilly\r\nGNU General Public License v3\r\n\r\nIf you use PRSice in any published work, please cite:\r\nJack Euesden Cathryn M. Lewis Paul F. O'Reilly (2015)\r\nPRSice: Polygenic Risk Score software.\r\nBioinformatics 31 (9): 1466-1468\r\n\r\n2018-12-20 16:48:46\r\n./PRSice_linux \\\r\n    --A1 A1 \\\r\n    --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \\\r\n    --base /home/cnap_lab_gwas/Downloads/try_2.assoc \\\r\n    --beta  \\\r\n    --binary-target F \\\r\n    --bp BP \\\r\n    --chr CHR \\\r\n    --clump-kb 250 \\\r\n    --clump-p 1.000000 \\\r\n    --clump-r2 0.100000 \\\r\n    --interval 5e-05 \\\r\n    --lower 0.0001 \\\r\n    --model add \\\r\n    --out /home/cnap_lab_gwas/mehul_PRS/HDL_mdrf_1912 \\\r\n    --pvalue P \\\r\n    --seed 154528568 \\\r\n    --snp SNP \\\r\n    --stat BETA \\\r\n    --target chr#_MDRF_hrcimputedbed,chr1_MDRF_hrcimputedbed.fam \\\r\n    --thread 1 \\\r\n    --type bed \\\r\n    --upper 0.5\r\n\r\n\r\nLoading Genotype file: \r\nchr#_MDRF_hrcimputedbed,chr1_MDRF_hrcimputedbed.fam (bed) \r\nWith external fam file: chr1_MDRF_hrcimputedbed.fam \r\n \r\n\r\n2059 people (0 male(s), 0 female(s)) observed \r\n2059 founder(s) included \r\n \r\n\r\n**Error: Currently do not support sample major format** \r\n\r\nError: \r\nExecution halted\r\n"}}
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