{"action":"created","issue":{"url":"https://api.github.com/repos/meren/anvio/issues/214","labels_url":"https://api.github.com/repos/meren/anvio/issues/214/labels{/name}","comments_url":"https://api.github.com/repos/meren/anvio/issues/214/comments","events_url":"https://api.github.com/repos/meren/anvio/issues/214/events","html_url":"https://github.com/meren/anvio/issues/214","id":111916210,"number":214,"title":"anvi-populate-genes-table error","user":{"login":"jgabriel1206","id":10200668,"avatar_url":"https://avatars.githubusercontent.com/u/10200668?v=3","gravatar_id":"","url":"https://api.github.com/users/jgabriel1206","html_url":"https://github.com/jgabriel1206","followers_url":"https://api.github.com/users/jgabriel1206/followers","following_url":"https://api.github.com/users/jgabriel1206/following{/other_user}","gists_url":"https://api.github.com/users/jgabriel1206/gists{/gist_id}","starred_url":"https://api.github.com/users/jgabriel1206/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jgabriel1206/subscriptions","organizations_url":"https://api.github.com/users/jgabriel1206/orgs","repos_url":"https://api.github.com/users/jgabriel1206/repos","events_url":"https://api.github.com/users/jgabriel1206/events{/privacy}","received_events_url":"https://api.github.com/users/jgabriel1206/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-10-16T21:42:19Z","updated_at":"2015-10-17T16:27:39Z","closed_at":null,"body":"Hi Meren\r\n\r\nI got this error when I tried to run anvi-populate-genes-table:\r\n\r\nFile/Path Error: Not all lines in the file 'svr_assign_to_dna_using_figfams.txt' have equal\r\n                 number of fields...\r\n\r\nI tried to fix this problem by using a simple awk command to replace spaces for _ in column 4, assuming that this was the issue:\r\n\r\nawk '{x=$4; gsub(/ /,\"_\",x); print $1,$2,$3,x,$5}' svr_assign_to_dna_using_figfams.txt > svr_assign_to_dna_using_figfams_awk.txt\r\n\r\nI tried to run the program again using the modified file but I got this new error:\r\n\r\nConfig Error: Mapping funciton '<type 'int'>' did not like the value '' in column number 2 of\r\n              the matrix :/\r\n\r\nDo you know why am I getting this error?\r\nThanks \r\nGabriel"},"comment":{"url":"https://api.github.com/repos/meren/anvio/issues/comments/148929547","html_url":"https://github.com/meren/anvio/issues/214#issuecomment-148929547","issue_url":"https://api.github.com/repos/meren/anvio/issues/214","id":148929547,"user":{"login":"jgabriel1206","id":10200668,"avatar_url":"https://avatars.githubusercontent.com/u/10200668?v=3","gravatar_id":"","url":"https://api.github.com/users/jgabriel1206","html_url":"https://github.com/jgabriel1206","followers_url":"https://api.github.com/users/jgabriel1206/followers","following_url":"https://api.github.com/users/jgabriel1206/following{/other_user}","gists_url":"https://api.github.com/users/jgabriel1206/gists{/gist_id}","starred_url":"https://api.github.com/users/jgabriel1206/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jgabriel1206/subscriptions","organizations_url":"https://api.github.com/users/jgabriel1206/orgs","repos_url":"https://api.github.com/users/jgabriel1206/repos","events_url":"https://api.github.com/users/jgabriel1206/events{/privacy}","received_events_url":"https://api.github.com/users/jgabriel1206/received_events","type":"User","site_admin":false},"created_at":"2015-10-17T16:27:39Z","updated_at":"2015-10-17T16:27:39Z","body":"Hi Meren\r\n\r\nI used the awk command and got this:\r\n\r\nawk 'BEGIN{FS=\"\\t\"}{print NF}' svr_assign_to_dna_using_figfams.txt | sort -n | uniq -c | sort -nr \r\n772683 5\r\n          1 1\r\nThen I tried again with anvi-populate-genes-table, but I got the same error:\r\n\r\nFile/Path Error: Not all lines in the file 'svr_assign_to_dna_using_figfams.txt' have equal\r\n                 number of fields...\r\n\r\nThanks\r\nGabriel"}}