<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="">Could you rerun with the latest MAKER release, just to make sure that it stil happens with the current release (Version 2.31.7). Run with 'maker -a’. If it still happenes, then send me the GFF3 files you are using as input, and I’ll take a look. Basically it’s happening because you are missing a start or end position for a feature in one of the files.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 19, 2014, at 5:47 AM, <a href="mailto:xiaenhua@gmail.com" class="">xiaenhua@gmail.com</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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 class=""></span><span style="background-color: rgba(0, 0, 0, 0);" class="">Dear Maker developer Team,<span class="Apple-converted-space"> </span><br class="">When I rerun maker using the first maker derived GFF3 files together with two newly generated evidence of Proteins and ESTs, I failed. I set the parameters in the maker_opt.ctl file like this:<span class="Apple-converted-space"> </span><br class="">-------------------------------------<span class="Apple-converted-space"> </span><br class="">genome=CSL.fasta<span class="Apple-converted-space"> </span><br class="">maker_gff=CSL_1st_maker.gff;<span class="Apple-converted-space"> </span><br class="">est_gff=osi_csl_maker.pasa_assemblies_Maker.gff3;<span class="Apple-converted-space"> </span><br class="">protein_gff=CSL_wise.gff3;<span class="Apple-converted-space"> </span><br class="">est2genome=1;<span class="Apple-converted-space"> </span><br class="">protein2genome=1;<span class="Apple-converted-space"> </span><br class="">other parameters with default.<span class="Apple-converted-space"> </span><br class="">Then, I run maker via MPI. However, during the 2nd run, I failed. Below is the error message:<span class="Apple-converted-space"> </span><br class="">-----------------------------------<span class="Apple-converted-space"> </span><br class="">preparing ab-inits<span class="Apple-converted-space"> </span><br class="">preparing ab-inits<span class="Apple-converted-space"> </span><br class="">preparing ab-inits<span class="Apple-converted-space"> </span><br class="">gathering ab-init output files<span class="Apple-converted-space"> </span><br class="">gathering ab-init output files<span class="Apple-converted-space"> </span><br class="">gathering ab-init output files<span class="Apple-converted-space"> </span><br class="">gathering ab-init output files<span class="Apple-converted-space"> </span><br class="">prepare section files<span class="Apple-converted-space"> </span><br class="">Gathering GFF3 input into hits - chunk:0<span class="Apple-converted-space"> </span><br class="">gathering ab-init output files<span class="Apple-converted-space"> </span><br class="">gathering ab-init output files<span class="Apple-converted-space"> </span><br class="">gathering ab-init output files<span class="Apple-converted-space"> </span><br class="">gathering ab-init output files<span class="Apple-converted-space"> </span><br class="">prepare section files<span class="Apple-converted-space"> </span><br class="">Gathering GFF3 input into hits - chunk:0<span class="Apple-converted-space"> </span><br class="">prepare section files<span class="Apple-converted-space"> </span><br class=""><font color="#ff0000" class="">Died at /home/xiaenhua/SoftWare/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.<span class="Apple-converted-space"> </span><br class="">--> rank=6, hostname=localhost.localdomain<span class="Apple-converted-space"> </span><br class="">ERROR: Failed while prepare section files<span class="Apple-converted-space"> </span><br class="">ERROR: Chunk failed at level:12, tier_type:3<span class="Apple-converted-space"> </span><br class="">FAILED CONTIG:scaffold3<span class="Apple-converted-space"> </span><br class=""><br class="">ERROR: Chunk failed at level:4, tier_type:0<span class="Apple-converted-space"> </span><br class="">FAILED CONTIG:scaffold3<span class="Apple-converted-space"> </span></font><br class=""><br class="">Gathering GFF3 input into hits - chunk:0<span class="Apple-converted-space"> </span><br class="">gathering ab-init output files<span class="Apple-converted-space"> </span><br class="">prepare section files<span class="Apple-converted-space"> </span><br class="">Gathering GFF3 input into hits - chunk:0<span class="Apple-converted-space"> </span><br class=""><font color="#ff0000" class="">Died at /home/xiaenhua/SoftWare/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.<span class="Apple-converted-space"> </span><br class="">--> rank=8, hostname=localhost.localdomain<span class="Apple-converted-space"> </span><br class="">ERROR: Failed while prepare section files<span class="Apple-converted-space"> </span><br class="">ERROR: Chunk failed at level:12, tier_type:3<span class="Apple-converted-space"> </span><br class="">FAILED CONTIG:scaffold5<span class="Apple-converted-space"> </span></font><br class=""><br class="">prepare section files<span class="Apple-converted-space"> </span><br class="">ERROR: Chunk failed at level:4, tier_type:0<span class="Apple-converted-space"> </span><br class="">FAILED CONTIG:scaffold5<span class="Apple-converted-space"> </span><br class="">........................<span class="Apple-converted-space"> </span><br class="">........................<span class="Apple-converted-space"> </span><br class="">-------------------------------------- </span></div><div style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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="background-color: rgba(0, 0, 0, 0);" class="">My protein evidence gff3 file looks like this:</span></div><div style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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="background-color: rgba(0, 0, 0, 0);" class="">scaffold3 genewise match 1276842 1277727 . - . ID=GeneWise.45.m<span class="Apple-converted-space"> </span><br class="">scaffold3 genewise match_part 1277687 1277727 . - . ID=GeneWise.45.cds_1;Parent=GeneWise.45.m <br class="">scaffold3 genewise match_part 1276842 1277545 . - . ID=GeneWise.45.cds_2;Parent=GeneWise.45.m</span></div><div style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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="background-color: rgba(0, 0, 0, 0);" class=""><br class=""></span></div><div style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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="background-color: rgba(0, 0, 0, 0);" class="">EST evidence gff3:</span></div><div style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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="background-color: rgba(0, 0, 0, 0);" class="">scaffold3 match 1275835 1276664 . + . ID=align_24718.m<span class="Apple-converted-space"> </span><br class="">scaffold3 match_part 1275835 1276664 . + . ID=align_24718.cds_1;Parent=align_24718.m<br class="">scaffold3 match 2510415 2511782 . + . ID=align_24719.m<span class="Apple-converted-space"> </span><br class="">scaffold3 match_part 2510415 2511782 . + . ID=align_24719.cds_1;Parent=align_24719.m<br class="">scaffold3 match 4113431 4114364 . + . ID=align_24720.m<span class="Apple-converted-space"> </span><br class="">scaffold3 match_part 4113431 4114364 . + . ID=align_24720.cds_1;Parent=align_24720.m<br class=""></span><span style="background-color: rgba(0, 0, 0, 0);" class=""><br class=""></span></div><div style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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="background-color: rgba(0, 0, 0, 0);" class="">I don't know what happened? Your any help will be appreciated greatly!<span class="Apple-converted-space"> </span><br class="">Thank you!<span class="Apple-converted-space"> </span><br class=""><br class="">All the best,<span class="Apple-converted-space"> </span><br class="">En-Hua Xia</span></div><span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 21px; 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=""></div></div></body></html>