{"action":"created","issue":{"url":"https://api.github.com/repos/molgenis/CoNVaDING/issues/30","repository_url":"https://api.github.com/repos/molgenis/CoNVaDING","labels_url":"https://api.github.com/repos/molgenis/CoNVaDING/issues/30/labels{/name}","comments_url":"https://api.github.com/repos/molgenis/CoNVaDING/issues/30/comments","events_url":"https://api.github.com/repos/molgenis/CoNVaDING/issues/30/events","html_url":"https://github.com/molgenis/CoNVaDING/issues/30","id":262114628,"number":30,"title":"StartWithBam - Uncaught exception","user":{"login":"rjsicko","id":7218576,"avatar_url":"https://avatars0.githubusercontent.com/u/7218576?v=4","gravatar_id":"","url":"https://api.github.com/users/rjsicko","html_url":"https://github.com/rjsicko","followers_url":"https://api.github.com/users/rjsicko/followers","following_url":"https://api.github.com/users/rjsicko/following{/other_user}","gists_url":"https://api.github.com/users/rjsicko/gists{/gist_id}","starred_url":"https://api.github.com/users/rjsicko/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rjsicko/subscriptions","organizations_url":"https://api.github.com/users/rjsicko/orgs","repos_url":"https://api.github.com/users/rjsicko/repos","events_url":"https://api.github.com/users/rjsicko/events{/privacy}","received_events_url":"https://api.github.com/users/rjsicko/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2017-10-02T14:58:46Z","updated_at":"2017-10-04T15:28:45Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI'm trying to test CoNVaDING v1.2.1 with data from a TruSeq Amplicon panel. I am getting the following error:\r\n````\r\nStarting analysis Mon Oct  2 10:48:56 2017\r\nReading BAM files to process..\r\nStarting counts analysis..\r\nUncaught exception from user code:\r\n\tChromosome name style in BED file does not correspond to naming style in BAM file. This is probably caused by using UCSC naming style in one file, and other naming style in the other file. Please fix your BED or BAM file chromosome naming.\r\n\tmain::countFromBam(\"/media/sf_BigShare/CFTR/convading_in/59_S1.bam\") called at ./CoNVaDING.pl line 723\r\n\tmain::startWithBam(ARRAY(0x13be840)) called at ./CoNVaDING.pl line 291\r\n````\r\n\r\nHowever, the bed file and bam seem to have a consistent naming style.\r\n\r\n**samtools view -H /media/sf_BigShare/CFTR/convading_in/59_S1.bam**\r\n````\r\n@HD\tVN:1.4\tSO:coordinate\r\n@PG\tID:Isis\r\n@SQ\tSN:chrM\tLN:16571\tM5:d2ed829b8a1628d16cbeee88e88e39eb\r\n@SQ\tSN:chr1\tLN:249250621\tM5:1b22b98cdeb4a9304cb5d48026a85128\r\n@SQ\tSN:chr2\tLN:243199373\tM5:a0d9851da00400dec1098a9255ac712e\r\n@SQ\tSN:chr3\tLN:198022430\tM5:641e4338fa8d52a5b781bd2a2c08d3c3\r\n@SQ\tSN:chr4\tLN:191154276\tM5:23dccd106897542ad87d2765d28a19a1\r\n@SQ\tSN:chr5\tLN:180915260\tM5:0740173db9ffd264d728f32784845cd7\r\n@SQ\tSN:chr6\tLN:171115067\tM5:1d3a93a248d92a729ee764823acbbc6b\r\n@SQ\tSN:chr7\tLN:159138663\tM5:618366e953d6aaad97dbe4777c29375e\r\n@SQ\tSN:chr8\tLN:146364022\tM5:96f514a9929e410c6651697bded59aec\r\n@SQ\tSN:chr9\tLN:141213431\tM5:3e273117f15e0a400f01055d9f393768\r\n@SQ\tSN:chr10\tLN:135534747\tM5:988c28e000e84c26d552359af1ea2e1d\r\n@SQ\tSN:chr11\tLN:135006516\tM5:98c59049a2df285c76ffb1c6db8f8b96\r\n@SQ\tSN:chr12\tLN:133851895\tM5:51851ac0e1a115847ad36449b0015864\r\n@SQ\tSN:chr13\tLN:115169878\tM5:283f8d7892baa81b510a015719ca7b0b\r\n@SQ\tSN:chr14\tLN:107349540\tM5:98f3cae32b2a2e9524bc19813927542e\r\n@SQ\tSN:chr15\tLN:102531392\tM5:e5645a794a8238215b2cd77acb95a078\r\n@SQ\tSN:chr16\tLN:90354753\tM5:fc9b1a7b42b97a864f56b348b06095e6\r\n@SQ\tSN:chr17\tLN:81195210\tM5:351f64d4f4f9ddd45b35336ad97aa6de\r\n@SQ\tSN:chr18\tLN:78077248\tM5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c\r\n@SQ\tSN:chr19\tLN:59128983\tM5:1aacd71f30db8e561810913e0b72636d\r\n@SQ\tSN:chr20\tLN:63025520\tM5:0dec9660ec1efaaf33281c0d5ea2560f\r\n@SQ\tSN:chr21\tLN:48129895\tM5:2979a6085bfe28e3ad6f552f361ed74d\r\n@SQ\tSN:chr22\tLN:51304566\tM5:a718acaa6135fdca8357d5bfe94211dd\r\n@SQ\tSN:chrX\tLN:155270560\tM5:7e0e2e580297b7764e31dbc80c2540dd\r\n@SQ\tSN:chrY\tLN:59373566\tM5:1e86411d73e6f00a10590f976be01623\r\n@RG\tID:59\tPL:ILLUMINA\tSM:59\r\n````\r\n**head -10 /media/sf_BigShare/CFTR/CFTR_clean_sorted.bed**\r\n\r\n````\r\nchr7\t117119879\t117120070\tCFTR\r\nchr7\t117120009\t117120240\tCFTR\r\nchr7\t117138266\t117138470\tCFTR\r\nchr7\t117144261\t117144461\tCFTR\r\nchr7\t117148936\t117149117\tCFTR\r\nchr7\t117149064\t117149287\tCFTR\r\nchr7\t117159379\t117159553\tCFTR\r\nchr7\t117170799\t117170982\tCFTR\r\nchr7\t117170923\t117171108\tCFTR\r\nchr7\t117171055\t117171257\tCFTR\r\n````\r\n"},"comment":{"url":"https://api.github.com/repos/molgenis/CoNVaDING/issues/comments/334194191","html_url":"https://github.com/molgenis/CoNVaDING/issues/30#issuecomment-334194191","issue_url":"https://api.github.com/repos/molgenis/CoNVaDING/issues/30","id":334194191,"user":{"login":"freerkvandijk","id":1861497,"avatar_url":"https://avatars0.githubusercontent.com/u/1861497?v=4","gravatar_id":"","url":"https://api.github.com/users/freerkvandijk","html_url":"https://github.com/freerkvandijk","followers_url":"https://api.github.com/users/freerkvandijk/followers","following_url":"https://api.github.com/users/freerkvandijk/following{/other_user}","gists_url":"https://api.github.com/users/freerkvandijk/gists{/gist_id}","starred_url":"https://api.github.com/users/freerkvandijk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/freerkvandijk/subscriptions","organizations_url":"https://api.github.com/users/freerkvandijk/orgs","repos_url":"https://api.github.com/users/freerkvandijk/repos","events_url":"https://api.github.com/users/freerkvandijk/events{/privacy}","received_events_url":"https://api.github.com/users/freerkvandijk/received_events","type":"User","site_admin":false},"created_at":"2017-10-04T15:28:45Z","updated_at":"2017-10-04T15:28:45Z","author_association":"MEMBER","body":"Good to hear my suggestion fixed your error. I'll check with the SAM format specifications if indeed our software was too stringent.\r\n\r\nRegarding your new question:\r\nsomething goes wrong in one of the regions of the CFTR gene:\r\nchr7   117119879   117120070    CFTR\r\nCould you maybe post a snippet of your BED file containing this line and the surrounding regions in the file?\r\n"}}
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