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Hi Irina,
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<div>Have you looked through your input for the duplicate IDs that the error talks about? It looks like some of your input files contain features with the same ID. </div>
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<div>~Daniel</div>
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<div>On Oct 24, 2014, at 7:17 AM, Irina Armean <<a href="mailto:iarmean@ebi.ac.uk">iarmean@ebi.ac.uk</a>> wrote:</div>
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<div dir="ltr">Dear all,<br>
<br>
I can't get a subset of <span tabindex="-1" id=":2n3.1" style="" class="">contigs</span> to finish, they keep failing.
<br>
<br>
The log below is of a 519 992 long and max_<span tabindex="-1" id=":2n3.2" style="" class="">dna</span>_<span tabindex="-1" id=":2n3.3" style="" class="">len</span>=100000. No
<span tabindex="-1" id=":2n3.4" style="" class="">gff</span> file is created. Just
<a href="http://evidence_0.gff.an/" target="_blank">evidence_0.<span tabindex="-1" id=":2n3.5" style="" class="">gff</span>.an</a> contains data (blast, protein2genome), the other 4 are empty (evidence_1, evidence_2, evidence_3, evidence_4).<br>
<br>
<br>
<font size="1">...processing 30 of 32<br>
...processing 31 of 32<br>
total clusters:5 now processing 0<br>
flattening protein clusters<br>
prepare section files<br>
Gathering GFF3 input into hits - chunk:0<br>
ERROR: Non-unique top level ID for<br>
While this is technically legal in GFF3, it usually<br>
indicates a poorly <span tabindex="-1" id=":2n3.6" style="" class="">fomatted</span> GFF3 file (perhaps you<br>
tried to merge two GFF3 files without accounting for<br>
unique IDs). MAKER will not handle these correctly.<br>
<br>
--> rank=NA, <span tabindex="-1" id=":2n3.7" style="" class="">hostname</span>=<a href="http://ebi3-202.ebi.ac.uk/" target="_blank">ebi3-202.<span tabindex="-1" id=":2n3.8" style="" class="">ebi</span>.ac.<span tabindex="-1" id=":2n3.9" style="" class="">uk</span></a><br>
ERROR: Failed while prepare section files<br>
ERROR: Chunk failed at level:12, tier_type:3<br>
FAILED <span tabindex="-1" id=":2n3.10" style="" class="">CONTIG</span>:scaffold2<br>
<br>
ERROR: Chunk failed at level:4, tier_type:0<br>
FAILED <span tabindex="-1" id=":2n3.11" style="" class="">CONTIG</span>:scaffold2<br>
<br>
examining contents of the <span tabindex="-1" id=":2n3.12" style="" class="">fasta</span> file and run log<br>
<br>
<br>
<br>
--Next <span tabindex="-1" id=":2n3.13" style="" class="">Contig</span>--</font><br>
<br>
Any suggestions much appreciated.<br>
<br>
Best wishes,<br>
Irina<br clear="all">
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-- <br>
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