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<p class="MsoNormal"><span style="font-size:11.0pt">Hey,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I have a problem getting maker to run.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I’ve tried installing the pipeline on three separate systems. CentOS 6 (cluster), Mac OS X 10.12.6 and on CentOS 7.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">With each of them I run into problems with Repeatmasker step with the error message:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">#---------------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Now starting the contig!!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">SeqID: chr0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Length: 38046352<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">#---------------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">setting up GFF3 output and fasta chunks<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">doing repeat masking<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">running repeat masker.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">#--------- command -------------#<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Widget::RepeatMasker:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">cd makertmp/maker_DMTHbJ; /Users/PM/maker/exe/RepeatMasker/RepeatMasker /Users/PM/GENEANNOTATION/TrR.v5.maker.output/TrR.v5_datastore/82/7E/chr0//theVoid.chr0/0/chr0.0.all.rb -species all -dir /Users/PM/GENEANNOTATION/TrR.v5.maker.output/TrR.v5_datastore/82/7E/chr0//theVoid.chr0/0
-pa 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">#-------------------------------#<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">doing blastx repeats<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">formating database...<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">#--------- command -------------#<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Widget::formater:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">/Users/PM/maker/bin/../exe/lblast/bin/makeblastdb -dbtype prot -in makertmp/maker_DMTHbJ/0/blastprep/te_proteins%2Efasta.mpi.10.0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">#-------------------------------#<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">BLAST options error: File makertmp/maker_DMTHbJ/0/blastprep/te_proteins%2Efasta.mpi.10.0 does not exist<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">ERROR: /Users/PM/maker/bin/../exe/lblast/bin/makeblastdb failed in Widget::formater<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">--> rank=NA, hostname=d24834.local<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">ERROR: Failed while doing blastx repeats<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">ERROR: Chunk failed at level:1, tier_type:1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">FAILED CONTIG:chr0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">ERROR: Chunk failed at level:2, tier_type:0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">FAILED CONTIG:chr0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">examining contents of the fasta file and run log<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">The Maker version that was installed is 2.31.9, and it was build using the ./Build commands.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">However the links for exonerate (2.2.0) and repeatmasker (repbase) (latest version) seem to be broken, as they always returned connection errors.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">So I manually installed both of those programs and linked maker to them.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I’ve attached the config files and the script used to run maker.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Marni Tausen<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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