{"action":"created","issue":{"url":"https://api.github.com/repos/combogenomics/medusa/issues/4","labels_url":"https://api.github.com/repos/combogenomics/medusa/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/combogenomics/medusa/issues/4/comments","events_url":"https://api.github.com/repos/combogenomics/medusa/issues/4/events","html_url":"https://github.com/combogenomics/medusa/issues/4","id":90284197,"number":4,"title":"ERROR: The reference file may contain sequences with non-unique header Ids","user":{"login":"genaev","id":769600,"avatar_url":"https://avatars.githubusercontent.com/u/769600?v=3","gravatar_id":"","url":"https://api.github.com/users/genaev","html_url":"https://github.com/genaev","followers_url":"https://api.github.com/users/genaev/followers","following_url":"https://api.github.com/users/genaev/following{/other_user}","gists_url":"https://api.github.com/users/genaev/gists{/gist_id}","starred_url":"https://api.github.com/users/genaev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/genaev/subscriptions","organizations_url":"https://api.github.com/users/genaev/orgs","repos_url":"https://api.github.com/users/genaev/repos","events_url":"https://api.github.com/users/genaev/events{/privacy}","received_events_url":"https://api.github.com/users/genaev/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-06-23T04:30:37Z","updated_at":"2015-06-24T07:48:34Z","closed_at":null,"body":"I launched the program and after several days of work got the error:\r\n```\r\n4: FINISHING DATA\r\nERROR: The reference file may contain sequences with non-unique\r\n       header Ids, please check your input files and try again\r\nERROR: postnuc returned non-zero\r\ndone.\r\n------------------------------------------------------------------------------------------------------------------------\r\nBuilding the network...\r\n```\r\nI check that reference not contain non-unique header:\r\nhow should I fix this?\r\n```\r\n[mag@smp medusa]$ cat reference_genomes/Canis_familiaris.fa | grep '>'\r\n>10 dna_rm:chromosome chromosome:CanFam3.1:10:1:69331447:1 REF\r\n>11 dna_rm:chromosome chromosome:CanFam3.1:11:1:74389097:1 REF\r\n>12 dna_rm:chromosome chromosome:CanFam3.1:12:1:72498081:1 REF\r\n>13 dna_rm:chromosome chromosome:CanFam3.1:13:1:63241923:1 REF\r\n>14 dna_rm:chromosome chromosome:CanFam3.1:14:1:60966679:1 REF\r\n>15 dna_rm:chromosome chromosome:CanFam3.1:15:1:64190966:1 REF\r\n>16 dna_rm:chromosome chromosome:CanFam3.1:16:1:59632846:1 REF\r\n>17 dna_rm:chromosome chromosome:CanFam3.1:17:1:64289059:1 REF\r\n>18 dna_rm:chromosome chromosome:CanFam3.1:18:1:55844845:1 REF\r\n>19 dna_rm:chromosome chromosome:CanFam3.1:19:1:53741614:1 REF\r\n>1 dna_rm:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF\r\n>20 dna_rm:chromosome chromosome:CanFam3.1:20:1:58134056:1 REF\r\n>21 dna_rm:chromosome chromosome:CanFam3.1:21:1:50858623:1 REF\r\n>22 dna_rm:chromosome chromosome:CanFam3.1:22:1:61439934:1 REF\r\n>23 dna_rm:chromosome chromosome:CanFam3.1:23:1:52294480:1 REF\r\n>24 dna_rm:chromosome chromosome:CanFam3.1:24:1:47698779:1 REF\r\n>25 dna_rm:chromosome chromosome:CanFam3.1:25:1:51628933:1 REF\r\n>26 dna_rm:chromosome chromosome:CanFam3.1:26:1:38964690:1 REF\r\n>27 dna_rm:chromosome chromosome:CanFam3.1:27:1:45876710:1 REF\r\n>28 dna_rm:chromosome chromosome:CanFam3.1:28:1:41182112:1 REF\r\n>29 dna_rm:chromosome chromosome:CanFam3.1:29:1:41845238:1 REF\r\n>2 dna_rm:chromosome chromosome:CanFam3.1:2:1:85426708:1 REF\r\n>30 dna_rm:chromosome chromosome:CanFam3.1:30:1:40214260:1 REF\r\n>31 dna_rm:chromosome chromosome:CanFam3.1:31:1:39895921:1 REF\r\n>32 dna_rm:chromosome chromosome:CanFam3.1:32:1:38810281:1 REF\r\n>33 dna_rm:chromosome chromosome:CanFam3.1:33:1:31377067:1 REF\r\n>34 dna_rm:chromosome chromosome:CanFam3.1:34:1:42124431:1 REF\r\n>35 dna_rm:chromosome chromosome:CanFam3.1:35:1:26524999:1 REF\r\n>36 dna_rm:chromosome chromosome:CanFam3.1:36:1:30810995:1 REF\r\n>37 dna_rm:chromosome chromosome:CanFam3.1:37:1:30902991:1 REF\r\n>38 dna_rm:chromosome chromosome:CanFam3.1:38:1:23914537:1 REF\r\n>3 dna_rm:chromosome chromosome:CanFam3.1:3:1:91889043:1 REF\r\n>4 dna_rm:chromosome chromosome:CanFam3.1:4:1:88276631:1 REF\r\n>5 dna_rm:chromosome chromosome:CanFam3.1:5:1:88915250:1 REF\r\n>6 dna_rm:chromosome chromosome:CanFam3.1:6:1:77573801:1 REF\r\n>7 dna_rm:chromosome chromosome:CanFam3.1:7:1:80974532:1 REF\r\n>8 dna_rm:chromosome chromosome:CanFam3.1:8:1:74330416:1 REF\r\n>9 dna_rm:chromosome chromosome:CanFam3.1:9:1:61074082:1 REF\r\n>X dna_rm:chromosome chromosome:CanFam3.1:X:1:123869142:1 REF\r\n```\r\n\r\nMoreover, I see the file \"nucmer.error\" which contains\r\n```\r\n20150623|091725| 29188| ERROR: postnuc returned non-zero\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/combogenomics/medusa/issues/comments/114769196","html_url":"https://github.com/combogenomics/medusa/issues/4#issuecomment-114769196","issue_url":"https://api.github.com/repos/combogenomics/medusa/issues/4","id":114769196,"user":{"login":"genaev","id":769600,"avatar_url":"https://avatars.githubusercontent.com/u/769600?v=3","gravatar_id":"","url":"https://api.github.com/users/genaev","html_url":"https://github.com/genaev","followers_url":"https://api.github.com/users/genaev/followers","following_url":"https://api.github.com/users/genaev/following{/other_user}","gists_url":"https://api.github.com/users/genaev/gists{/gist_id}","starred_url":"https://api.github.com/users/genaev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/genaev/subscriptions","organizations_url":"https://api.github.com/users/genaev/orgs","repos_url":"https://api.github.com/users/genaev/repos","events_url":"https://api.github.com/users/genaev/events{/privacy}","received_events_url":"https://api.github.com/users/genaev/received_events","type":"User","site_admin":false},"created_at":"2015-06-24T07:48:34Z","updated_at":"2015-06-24T07:48:34Z","body":"the comman line:\r\n```\r\n$ java -jar ~/prog/medusa/medusa.jar -f reference_genomes/ -i L_RNA_scaffolder_20150415-aligngraph-lastz-blat.fasta -o L_RNA_scaffolder_20150415-aligngraph-lastz-blat-medusa.fasta -v 1>medusa.out 2>medusa.err\r\n```\r\nthe list of reference genomes (only one):\r\n```\r\n$ ls -l reference_genomes/\r\nитого 2311230\r\n-rw-rw-r-- 1 mag mag 2366430334 Июн 23 11:28 Canis_familiaris_rename.fa\r\n```\r\nthe first ten lines of query genome and reference genomes:\r\n```\r\n$ head -10 L_RNA_scaffolder_20150415-aligngraph-lastz-blat.fasta \r\n>AlignGraph0 @ chr1 : Contig56154 ; Contig112286 ; \r\nCCTGGGCTGGCCTGGCCCCGGGCTCTGTGGGGGCAGGGGCGACTCGAGCGCCTGCCCCAG\r\nGCCCAGCGCTAATGGGATCCAGCGCCCCGGGGCCCTGGCCAGGCCTGCGTTCTGGCCCCG\r\nGGCTGAGCGAGCCCTCTCACAGCAGGATGTGGCCTCCTGGGCCCTGGGCGTGCCCCACAG\r\nACCCAGGTCGCTGACCTAGGGCAGCCCTGGGGATCCCAGGACACCCCAGGGCAGGGCAGC\r\nGGGGGCAGGCCCGTGGGCCCCACCCACACCCACACCCACACCCACACCCACACCCACACC\r\nAGGAGGCAGGCTCCTCCACGTGCTGGGGCTCCAGGGGGCCCGAGGCCGGGGTCCAGGTGC\r\nCCTGCGGGGACCCAGCGCAGGAGCCCATGGGCCGCAGGTCCACGTCAGCCCTGCCGCCCC\r\nCAGAACCGCCTCTCACCGCCCCGACCTCAGGACACGCGCCCCCACCCGGAGTCCACACAG\r\nGCTCCCAGGTGGGGGACTCCAGCACCCGCCTCCCCACCCCGTGGGATTCTTGCCCTCCCC\r\n\r\n$ head -10 reference_genomes/Canis_familiaris_rename.fa \r\n>1_10dna_rm:chromosomechromosome:CanFam3.1:10:1:69331447:1REF\r\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\r\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\r\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\r\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\r\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\r\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\r\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\r\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\r\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\r\n```"}}