<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">You need to rename the contig. It is currently named 0<div class=""><br class=""></div><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><div class=""><br class=""></div><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><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><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><br class="Apple-interchange-newline"><div class=""><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">Dear Maker,<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">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><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">Here is the error I get:</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">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="http://dee-serv04.vital-it.ch/" 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><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">Any thought how to solve this?</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">Thanks in advance,</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">Victor Rossier<span class="Apple-converted-space"> </span><br class=""></div><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><a href="mailto:maker-devel@box290.bluehost.com" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">maker-devel@box290.bluehost.com</a><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: 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; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""></div></blockquote></div><br class=""></div></div></body></html>