{"action":"created","issue":{"url":"https://api.github.com/repos/cfljam/galaxy-pcr-markers/issues/29","labels_url":"https://api.github.com/repos/cfljam/galaxy-pcr-markers/issues/29/labels{/name}","comments_url":"https://api.github.com/repos/cfljam/galaxy-pcr-markers/issues/29/comments","events_url":"https://api.github.com/repos/cfljam/galaxy-pcr-markers/issues/29/events","html_url":"https://github.com/cfljam/galaxy-pcr-markers/issues/29","id":87143453,"number":29,"title":"Issue with design_primers.py","user":{"login":"rtraborn","id":5387723,"avatar_url":"https://avatars.githubusercontent.com/u/5387723?v=3","gravatar_id":"","url":"https://api.github.com/users/rtraborn","html_url":"https://github.com/rtraborn","followers_url":"https://api.github.com/users/rtraborn/followers","following_url":"https://api.github.com/users/rtraborn/following{/other_user}","gists_url":"https://api.github.com/users/rtraborn/gists{/gist_id}","starred_url":"https://api.github.com/users/rtraborn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rtraborn/subscriptions","organizations_url":"https://api.github.com/users/rtraborn/orgs","repos_url":"https://api.github.com/users/rtraborn/repos","events_url":"https://api.github.com/users/rtraborn/events{/privacy}","received_events_url":"https://api.github.com/users/rtraborn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2015-06-10T23:29:58Z","updated_at":"2015-07-01T17:00:41Z","closed_at":null,"body":"Hi:\r\nI'm having trouble executing the program using your test data from [your iPython notebook](http://nbviewer.ipython.org/gist/cfljam/5892919/Designing%20CAPS%20Markers.ipynb).\r\n\r\nAfter installing primer3 and cloning your repo, I ran the command exactly as indicated:\r\n`python design_primers.py -i test-data/targets.fasta -g test-data/targets.gff -T Taq1CAPS.out -p 80 -P 150 -n 1`\r\n\r\nHowever, I get the following error:\r\n```SNP_Target_ID Position Ref_base Variant_base Amplicon_bp PRIMER_LEFT_SEQUENCE PRIMER_RIGHT_SEQUENCE ref_melt_Tm var_melt_Tm Tm_difference\r\nTraceback (most recent call last):\r\n  File \"design_primers.py\", line 154, in <module>\r\n    result=P3.run_P3(target_dict=my_target_dict)\r\n  File \"/nfs4shares/jumen_share/lbui/galaxy-pcr-markers/run_p3.py\", line 39, in run_P3\r\n    output = sp.check_output(input_str,shell=True)\r\n  File \"/nfs4shares/jumen_share/lbui/galaxy-pcr-markers/run_p3.py\", line 21, in f\r\n    raise sp.CalledProcessError(retcode,cmd)\r\nsubprocess.CalledProcessError: Command 'echo  \"SEQUENCE_TARGET=150,1\r\nPRIMER_MAX_POLY_X=3\r\nPRIMER_PAIR_MAX_DIFF_TM=1\r\nPRIMER_MAX_GC=80.0\r\nPRIMER_MIN_GC=20.0\r\nPRIMER_OPT_SIZE=20\r\nSEQUENCE_ID=k69_93535\r\nSEQUENCE_EXCLUDED_REGION=144,2\r\nPRIMER_MAX_SIZE=25\r\nPRIMER_OPT_GC_PERCENT=50\r\nPRIMER_OPT_TM=59\r\nPRIMER_MAX_NS_ACCEPTED=1\r\nPRIMER_GC_CLAMP=1\r\nPRIMER_MIN_SIZE=18\r\nPRIMER_MAX_SELF_ANY=8\r\nPRIMER_NUM_RETURN=2\r\nSEQUENCE_TEMPLATE=TGCTAATGACAACGAGGAGGTAGAATCTGGAGATGAATCAGACTCTTCAGTTGCTTCCTGCCCTCCTACACTTAATGAAGGAAAGAAAAAAAGGACAGGGAAGCTTCATAGGCCTTTGAGTCTGAACGCATTTGACATAATTTCCTTTTCCAGAGGATTTGATCTTTCAGGTTTGTTTGAAGAAACGGGAGATGAAACAAGATTTGTGTCGGGTGAAACGATACCAAACATCATATCGAAATTGGAGGAGATTGCAAAAGTGGGTAGTTTCACGTTTAGGAAGAAGGATTGTAGGGTTAG\r\nPRIMER_PRODUCT_SIZE_RANGE=80-150\r\nPRIMER_MAX_SELF_END=3\r\n=\" | primer3_core ' returned non-zero exit status 255```\r\n\r\nI reproduced this error using other input data and on another machine. Could you look into this when you have the chance? Thanks!\r\n"},"comment":{"url":"https://api.github.com/repos/cfljam/galaxy-pcr-markers/issues/comments/117751579","html_url":"https://github.com/cfljam/galaxy-pcr-markers/issues/29#issuecomment-117751579","issue_url":"https://api.github.com/repos/cfljam/galaxy-pcr-markers/issues/29","id":117751579,"user":{"login":"lo2811","id":12261634,"avatar_url":"https://avatars.githubusercontent.com/u/12261634?v=3","gravatar_id":"","url":"https://api.github.com/users/lo2811","html_url":"https://github.com/lo2811","followers_url":"https://api.github.com/users/lo2811/followers","following_url":"https://api.github.com/users/lo2811/following{/other_user}","gists_url":"https://api.github.com/users/lo2811/gists{/gist_id}","starred_url":"https://api.github.com/users/lo2811/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lo2811/subscriptions","organizations_url":"https://api.github.com/users/lo2811/orgs","repos_url":"https://api.github.com/users/lo2811/repos","events_url":"https://api.github.com/users/lo2811/events{/privacy}","received_events_url":"https://api.github.com/users/lo2811/received_events","type":"User","site_admin":false},"created_at":"2015-07-01T17:00:40Z","updated_at":"2015-07-01T17:00:40Z","body":"Hi John,\r\n\r\nI ran it on unix windows machine, and my fiancé tried it on a mac. I reran the script as in your suggestion, but still got the same error as before.\r\n\r\nMy guess is that I will have to use your docker image. I’ll keep you updated.\r\n\r\nThank you!\r\n\r\nLinh\r\n\r\nFrom: John McCallum [mailto:notifications@github.com]\r\nSent: Tuesday, June 30, 2015 6:26 PM\r\nTo: cfljam/galaxy-pcr-markers\r\nCc: Bui, Linh\r\nSubject: Re: [galaxy-pcr-markers] Issue with design_primers.py (#29)\r\n\r\n\r\nWas this run on a unix or osx or windows machine?\r\n\r\n—\r\nReply to this email directly or view it on GitHub<https://github.com/cfljam/galaxy-pcr-markers/issues/29#issuecomment-117371460>.\r\n"}}