{"action":"created","issue":{"url":"https://api.github.com/repos/ekg/freebayes/issues/180","labels_url":"https://api.github.com/repos/ekg/freebayes/issues/180/labels{/name}","comments_url":"https://api.github.com/repos/ekg/freebayes/issues/180/comments","events_url":"https://api.github.com/repos/ekg/freebayes/issues/180/events","html_url":"https://github.com/ekg/freebayes/issues/180","id":93872622,"number":180,"title":"dDocent std::out_of_range error","user":{"login":"jsage8","id":8370228,"avatar_url":"https://avatars.githubusercontent.com/u/8370228?v=3","gravatar_id":"","url":"https://api.github.com/users/jsage8","html_url":"https://github.com/jsage8","followers_url":"https://api.github.com/users/jsage8/followers","following_url":"https://api.github.com/users/jsage8/following{/other_user}","gists_url":"https://api.github.com/users/jsage8/gists{/gist_id}","starred_url":"https://api.github.com/users/jsage8/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jsage8/subscriptions","organizations_url":"https://api.github.com/users/jsage8/orgs","repos_url":"https://api.github.com/users/jsage8/repos","events_url":"https://api.github.com/users/jsage8/events{/privacy}","received_events_url":"https://api.github.com/users/jsage8/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-07-08T19:39:01Z","updated_at":"2015-07-13T17:05:37Z","closed_at":null,"body":"I am using the dDocent pipeline that includes freebayes as a pen-ultimate step. Every other portion of the pipeline seems to complete successfully, then freebayes runs for several hours running in gnu parallel. I then get an our of range error like the following:\r\n\r\nERROR(freebayes): Target region coordinates (uti_cns_0004702 241471852 241471871) outside of reference sequence bounds (uti_cns_0004702 783485) terminating.\r\nterminate called after throwing an instance of 'std::out_of_range'\r\n  what():  basic_string::substr\r\n\r\nThe line that runs freebayes in dDocent looks like this:\r\n\r\nls mapped.*.bed | sed 's/mapped.//g' | sed 's/.bed//g' | shuf | parallel --memfree $MAXMemory -j $FB1 --noswap --no-notice --delay 1 freebayes -L bamlist.list -t mapped.{}.bed -v raw.{}.vcf -f reference.fasta -m 5 -q 5 -E 3 --experimental-gls --min-repeat-entropy 1 -V --populations popmap -n 10\r\n\r\nWhere $MAXMemory is a memory amount postfixed by G for gigabytes, $FB1 is the number of processors to allocate to freebayes instances. The bed and vcf files are filled in by the files that are in the working directory.\r\n\r\nI've checked in with the creator of dDocent already, but I figured you may have some more specific input."},"comment":{"url":"https://api.github.com/repos/ekg/freebayes/issues/comments/120994559","html_url":"https://github.com/ekg/freebayes/issues/180#issuecomment-120994559","issue_url":"https://api.github.com/repos/ekg/freebayes/issues/180","id":120994559,"user":{"login":"jsage8","id":8370228,"avatar_url":"https://avatars.githubusercontent.com/u/8370228?v=3","gravatar_id":"","url":"https://api.github.com/users/jsage8","html_url":"https://github.com/jsage8","followers_url":"https://api.github.com/users/jsage8/followers","following_url":"https://api.github.com/users/jsage8/following{/other_user}","gists_url":"https://api.github.com/users/jsage8/gists{/gist_id}","starred_url":"https://api.github.com/users/jsage8/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jsage8/subscriptions","organizations_url":"https://api.github.com/users/jsage8/orgs","repos_url":"https://api.github.com/users/jsage8/repos","events_url":"https://api.github.com/users/jsage8/events{/privacy}","received_events_url":"https://api.github.com/users/jsage8/received_events","type":"User","site_admin":false},"created_at":"2015-07-13T17:05:37Z","updated_at":"2015-07-13T17:05:37Z","body":"I also ran this command:\r\n\r\ngrep -A1 'uti_cns_0004702' reference-spinach_genomeV.fasta | grep -v 'uti_cns_0004702' | wc -m\r\n\r\nto determine how long uti_cns_0004702 actually is and the output was 502295897. So the coordinates it's trying to access are within the bounds of that contig."}}