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<p class="MsoNormal">Hi Gez,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m forwarding you e-mail to the maker-devel mailing list for support. This mailing list is a good place to direct questions like this one. If you aren’t aleady a member of this mailing list, I’d highly recommend you join here:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><a href="http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Cheers,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Barry<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Gezahegn Girma <ggirmate@purdue.edu><br>
<b>Date: </b>Thursday, October 28, 2021 at 12:19 PM<br>
<b>To: </b>Marvin B Moore <barry.moore@genetics.utah.edu><br>
<b>Subject: </b>Support on maker<o:p></o:p></span></p>
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<p class="MsoNormal">Hi Barry,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I am using maker for genome annotation of sorghum genotype.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Maker is running and keep increasing the log file but I see the following error messages. Kindly, this is to request for your kind support to resolve this issue.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">=========================================================<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Courier">STATUS: Now running MAKER...</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier;color:red">WARNING: Cannot find >0, trying to re-index the fasta.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier;color:red">stop here: 0</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier;color:red">ERROR: Fasta index error</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier"> at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier"> Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier">10-nompi/bin/../lib/Process/MpiTiers.pm line 73</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier"> <span class="apple-tab-span">
</span> <span class="apple-tab-span"> </span> Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415</span><o:p></o:p></p>
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</span> eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier"> <span class="apple-tab-span">
</span> <span class="apple-tab-span"> </span> </span><span style="font-size:10.0pt;font-family:Courier;color:red">Error::subs::try(CODE(0x5e89c60), HASH(0x5e8f6f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiT</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier;color:red">iers.pm line 79</span><o:p></o:p></p>
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</span>Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier">Process/MpiTiers.pm line 56</span><o:p></o:p></p>
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</span> Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier">1.10-nompi/bin/maker line 669</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier">--> rank=NA, hostname=<a href="http://bell-a105.rcac.purdue.edu">bell-a105.rcac.purdue.edu</a></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier;color:red">ERROR: Failed in tier preparation</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier">examining contents of the fasta file and run log</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier">.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier">.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier">.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier;color:red">Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid
query sequence or its </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier">translation. Please verify the query sequence(s) and/or filtering options</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Courier">deleted:0 hits</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt">================================================================================</span><o:p></o:p></p>
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<p class="MsoNormal">Regards,<o:p></o:p></p>
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<p class="MsoNormal">Gez<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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