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<meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hello,</div><div class=""><br class=""></div><div class="">I am using maker for genome annotation of sorghum genotype.</div><div class=""><br class=""></div><div class="">Maker is running and keep increasing the log file but I see the following error messages. This is to request for your kind support to resolve this issue.</div><div class=""><br class=""></div><div class="">=========================================================</div><div class=""><span class="" style="font-family: Courier; font-size: 10pt;"><span class="Apple-tab-span" style="white-space: pre;"> </span>STATUS: Now running MAKER...</span></div><div class=""><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier; color: red;"><span class="Apple-tab-span" style="white-space: pre;"> </span>WARNING: Cannot find >0, trying to re-index the fasta.<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier; color: red;"><span class="Apple-tab-span" style="white-space: pre;"> </span>stop here: 0<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier; color: red;"><span class="Apple-tab-span" style="white-space: pre;"> </span>ERROR: Fasta index error<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span> at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239.<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span> Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31.<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span>10-nompi/bin/../lib/Process/MpiTiers.pm line 73<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"> <span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"> <span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> </span><span class="" style="font-size: 10pt; 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<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier; color: red;"><span class="Apple-tab-span" style="white-space: pre;"> </span>iers.pm line 79<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"> <span class="Apple-tab-span" style="white-space: pre;"> </span>Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span>Process/MpiTiers.pm line 56<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"> <span class="Apple-tab-span" style="white-space: pre;"> </span> Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span>1.10-nompi/bin/maker line 669<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span>--> rank=NA, hostname=<a href="http://bell-a105.rcac.purdue.edu" class="">bell-a105.rcac.purdue.edu</a><o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier; color: red;"><span class="Apple-tab-span" style="white-space: pre;"> </span>ERROR: Failed in tier preparation<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span>examining contents of the fasta file and run log<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span>.<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span>.<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span>.<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier; color: red;"><span class="Apple-tab-span" style="white-space: pre;"> </span>Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence <span class="Apple-tab-span" style="white-space: pre;"> </span>or its <span class="Apple-tab-span" style="white-space: pre;"> </span></span></p><p class="MsoNormal"><span class="" style="font-family: Courier; font-size: 10pt;"><span class="Apple-tab-span" style="white-space: pre;"> </span>translation. Please verify the query sequence(s) and/or filtering options</span></p><p class="MsoNormal"><span class="" style="font-size: 10pt; font-family: Courier;"><span class="Apple-tab-span" style="white-space: pre;"> </span>deleted:0 hits<o:p class=""></o:p></span></p><p class="MsoNormal"><span class="" style="font-size: 10pt;">================================================================================</span></p><div class=""><div class="">Regards,</div><div class="">Gez</div></div></div></body></html>