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<p>Thanks for the quick replies,</p>
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<p>It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'.</p>
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<p>I renamed all transcripts and maker finished correctly!</p>
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<p>Thanks again,</p>
<p>Victor Rossier<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>De :</b> Fields, Christopher J <cjfields@illinois.edu><br>
<b>Envoyé :</b> mercredi 6 juillet 2016 14:16<br>
<b>À :</b> Carson Holt<br>
<b>Cc :</b> Victor Rossier; maker-devel@yandell-lab.org<br>
<b>Objet :</b> Re: [maker-devel] Fasta index error</font>
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<div class="">I’ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. </div>
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<div class="">chris</div>
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<div class="">On Jul 5, 2016, at 9:29 AM, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:</div>
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<div class="" style="word-wrap:break-word">You need to rename the contig. It is currently named 0
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<div class="">The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it’s the kind of thing that has the potential to cause
errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed.</div>
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<div class="">You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference.</div>
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<div class="">—Carson</div>
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<div class="">On Jul 4, 2016, at 9:38 AM, Victor Rossier <<a href="mailto:Victor.Rossier@unil.ch" class="">Victor.Rossier@unil.ch</a>> wrote:</div>
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<div class="" style="margin-top:0px; margin-bottom:0px; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; background-color:rgb(255,255,255)">
Dear Maker,<span class="Apple-converted-space"> </span></div>
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I did run maker for the annotation of a<span class="Apple-converted-space"> </span><em class="">denovo</em><span class="Apple-converted-space"> </span>genome assembly. It works great for all scaffolds but 1.</div>
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Here is the error I get:</div>
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WARNING: Cannot find >0, trying to re-index the fasta.<br class="">
stop here:0<br class="">
ERROR: Fasta index error<br class="">
at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622.<br class="">
GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...',
...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491<br class="">
Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415<br class="">
eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407<br class="">
Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224<br class="">
Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341<br class="">
Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979<br class="">
--> rank=16, hostname=<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__dee-2Dserv04.vital-2Dit.ch_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=IMqKG5fcHs_DVo3tdSTcbqMWVKDw9ntAr8RMBGD45_M&s=KvnplP4Ch4nKxsCIW-K3rDj6OLpTNh1ND6cgWYs24U8&e=" class="">dee-serv04.vital-it.ch</a><br class="">
ERROR: Failed while polishing alt-ESTs<br class="">
ERROR: Chunk failed at level:6, tier_type:3<br class="">
FAILED CONTIG:scaffold52256_cov106<br class="">
<br class="">
ERROR: Chunk failed at level:4, tier_type:0<br class="">
FAILED CONTIG:scaffold52256_cov106</div>
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Any thought how to solve this?</div>
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Thanks in advance,</div>
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Victor Rossier<span class="Apple-converted-space"> </span><br class="">
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