<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=""><div class="">Separate out just that contig into a separate file and run it by itself. You may also want to rename the contig. Don’t call it 0. Having the name simply be a zero has the potential to cause any number of problems in MAKER or any of the programs MAKER uses because 0 all by itself means ‘false’ in most computer languages. Try contig_0 instead. It looks like the first error may be the BioPerl indexer failing because the contig is named 0.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 30, 2015, at 2:52 AM, 尹传林 <<a href="mailto:yincl2013@126.com" class="">yincl2013@126.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><stationery style="font-family: simsun, serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class=""><div class=""><font face="Times New Roman" class="">Hello, </font></div><div class=""><font face="Times New Roman" class=""></font> </div><div class=""><font face="Times New Roman" class="">When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I donot konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. </font></div><div class=""><font face="Times New Roman" class=""></font> </div><div class=""><font face="Times New Roman" class="">Here is a part of main error log: </font></div><blockquote dir="ltr" style="margin: 0px 0px 0px 2em;" class=""><div class=""><font face="Times New Roman" class="">WARNING: Cannot find >0, trying to re-index the fasta. </font></div><div class=""><font face="Times New Roman" class="">stop here:0 </font></div><div class=""><font face="Times New Roman" class="">ERROR: Fasta index error </font></div><div class=""><font face="Times New Roman" class=""> at /disk/yinchuanlin/software/maker/maker/bin/../lib/GI.pm line 1622. </font></div><div class=""><font face="Times New Roman" class=""> GI::polish_exonerate(FastaChunk=HASH(0x7fe0263563b8), FastaSeq=HASH(0x3f7b280), 2988503, ">contig1", ARRAY(0x3d3ad80), ARRAY(0x3d17ed0), "/disk/yinchuanlin/01_pingguodue_project/02_OMIGA/09_maker_wor"..., "e", "/disk/yinchuanlin/software/maker/exonerate-2.2.0-x86_64/bin/e"..., ...) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiChunk.pm line 1986 </font></div><div class=""><font face="Times New Roman" class=""> Process::MpiChunk::__ANON__() called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Error.pm line 415 </font></div><div class=""><font face="Times New Roman" class=""> eval {...} called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Error.pm line 407 </font></div><div class=""><font face="Times New Roman" class=""> Error::subs::try(CODE(0x3f381b8), HASH(0x3f62380)) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiChunk.pm line 4224 </font></div><div class=""><font face="Times New Roman" class=""> Process::MpiChunk::_go(Process::MpiChunk=HASH(0x3e30020), "run", HASH(0x7fe026352410), 2, 3) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiChunk.pm line 341 </font></div><div class=""><font face="Times New Roman" class=""> Process::MpiChunk::run(Process::MpiChunk=HASH(0x3e30020), 0) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiChunk.pm line 357 </font></div><div class=""><font face="Times New Roman" class=""> Process::MpiChunk::run_all(Process::MpiChunk=HASH(0x3e30020), 0) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiTiers.pm line 287 </font></div><div class=""><font face="Times New Roman" class=""> Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x3d43310), 0) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiTiers.pm line 287 </font></div><div class=""><font face="Times New Roman" class=""> Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x3f28b28), 0) called at /disk/yinchuanlin/software/maker/maker/bin/maker line 686 </font></div><div class=""><font face="Times New Roman" class="">--> rank=NA, hostname=node7 </font></div><div class=""><font face="Times New Roman" class="">ERROR: Failed while polishig ESTs </font></div><div class=""><font face="Times New Roman" class="">ERROR: Chunk failed at level:2, tier_type:3 </font></div><div class=""><font face="Times New Roman" class="">FAILED CONTIG:contig1 </font></div><div class=""><font face="Times New Roman" class=""></font> </div><div class=""><font face="Times New Roman" class="">ERROR: Chunk failed at level:4, tier_type:0 </font></div><div class=""><font face="Times New Roman" class="">FAILED CONTIG:contig1 </font></div></blockquote><div class=""><font face="Times New Roman" class=""></font> </div><div class=""><font face="Times New Roman" class="">Thanks! </font></div><div class=""><font face="Times New Roman" class=""></font> </div><div class=""><font face="Times New Roman" class="">Best regards, </font></div><div class=""><font face="Times New Roman" class="">Ian </font></div><div class=""><font face="Times New Roman" class="">Department of Entomology, College of Plant Protection, Nanjing Agricultural University </font></div><div class=""><font face="Times New Roman" class="">No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China </font></div><div class=""><font face="Times New Roman" class=""></font> </div><div class=""><font face="Times New Roman" class=""></font> </div></div></stationery><span style="font-family: simsun, serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: simsun, serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: simsun, serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="font-family: simsun, serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:maker-devel@box290.bluehost.com" style="font-family: simsun, serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">maker-devel@box290.bluehost.com</a><br style="font-family: simsun, serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" style="font-family: simsun, serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></body></html>