{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/423","repository_url":"https://api.github.com/repos/broadinstitute/viral-ngs","labels_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/423/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/423/comments","events_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/423/events","html_url":"https://github.com/broadinstitute/viral-ngs/issues/423","id":168224461,"number":423,"title":"snpEff requires LC_ALL=C","user":{"login":"haydenm","id":3084862,"avatar_url":"https://avatars.githubusercontent.com/u/3084862?v=3","gravatar_id":"","url":"https://api.github.com/users/haydenm","html_url":"https://github.com/haydenm","followers_url":"https://api.github.com/users/haydenm/followers","following_url":"https://api.github.com/users/haydenm/following{/other_user}","gists_url":"https://api.github.com/users/haydenm/gists{/gist_id}","starred_url":"https://api.github.com/users/haydenm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/haydenm/subscriptions","organizations_url":"https://api.github.com/users/haydenm/orgs","repos_url":"https://api.github.com/users/haydenm/repos","events_url":"https://api.github.com/users/haydenm/events{/privacy}","received_events_url":"https://api.github.com/users/haydenm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-07-29T00:09:30Z","updated_at":"2016-07-29T13:09:33Z","closed_at":null,"body":"`snpEff` gave me an error related to coordinates. Changing `LC_ALL` from `en_US.utf8` to `C` fixed this. The issue might relate to a use of GNU `sort`. Perhaps we can set `LC_ALL` to `C` for just the call to `snpEff`?"},"comment":{"url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/comments/236175867","html_url":"https://github.com/broadinstitute/viral-ngs/issues/423#issuecomment-236175867","issue_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/423","id":236175867,"user":{"login":"dpark01","id":8513746,"avatar_url":"https://avatars.githubusercontent.com/u/8513746?v=3","gravatar_id":"","url":"https://api.github.com/users/dpark01","html_url":"https://github.com/dpark01","followers_url":"https://api.github.com/users/dpark01/followers","following_url":"https://api.github.com/users/dpark01/following{/other_user}","gists_url":"https://api.github.com/users/dpark01/gists{/gist_id}","starred_url":"https://api.github.com/users/dpark01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpark01/subscriptions","organizations_url":"https://api.github.com/users/dpark01/orgs","repos_url":"https://api.github.com/users/dpark01/repos","events_url":"https://api.github.com/users/dpark01/events{/privacy}","received_events_url":"https://api.github.com/users/dpark01/received_events","type":"User","site_admin":false},"created_at":"2016-07-29T13:09:33Z","updated_at":"2016-07-29T13:09:33Z","body":"This may be a separate issue then? Sounds as if your VCF (which you made yourself) is not sorted -- it's complaining that your variants are not grouped by chromosome\n\n--\nDaniel J. Park, PhD\nGroup Leader, Viral Computational Genomics\nBroad Institute of MIT and Harvard\nTel: +1-617-714-8526\ndpark@broadinstitute.org\nhttp://www.broadinstitute.org/bios/daniel-park\n\n> On Jul 29, 2016, at 9:01 AM, haydenm <notifications@github.com> wrote:\n> \n> I'm confused now because I just tried to replicate this and could not (I did not try before posting). Here was the error I got:\n> \n> 2016-07-28 19:01:16,416 - snpeff:61:execute - DEBUG - /idi/sabeti-scratch/hmetsky/viral-ngs/viral-ngs-etc/conda-env/bin/snpEff -Xmx4g -Djava.io.tmpdir=/tmp/2428303.1.short/tmp-interhost-snpEff-yn_v_qrx ann -treatAllAsProteinCoding false -t -noLog -ud 0 -noStats -noShiftHgvs d40f92b7319a741b3cebf4ecaa016b7e33e118034ac3f0d15fde971 /idi/sabeti-scratch/hmetsky/viral-work/results/viral-ngs/zika/clinical-samples/zika_brazil_fiocruz-thiago/data/03_align_to_ref/B4-HS-hiseq.for_snpeff.vcf.gz\n> [E::get_intv] failed to parse TBX_VCF, was wrong -p [type] used?\n> The offending line was: \"Error: Error while processing VCF entry (line 289) :\"\n> [E::hts_idx_push] chromosome blocks not continuous\n> \n> The one change I made after seeing this was export LC_ALL=C before re-running and having it succeed. I notice now that one of the top lines of conda-env/bin/snpEff is export LC_ALL=en_US.UTF-8, so it might be involved somehow. Sorry for the confusion; I'm not sure why I can't replicate this, and I don't have anything to add to help replicate it.\n> \n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub, or mute the thread.\n> \n"}}
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