<html><head><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="">Hi,<div class=""><br class=""></div><div class="">I am using maker to do repeat masking and genome annotation. So far I have assembly, est and protein evidence. What I did is use maker to initialized three files and only edit the maker_opts.ctl. I put the genome, est and proteins. Also I changed the est2geome=1 and protein2gemone=1. But what I got is always wrong. I used the high performance cluster in our university and it is already installed MPI with maker. Error showed like this .</div><div class="">I am a little confused about that should maker cannot do repeat masking automatically for me? I have to use RepeatModeler/RepeatMasker to do that first then use maker and skip the repeat masking? Or I have to make the specific repeat library and this is also a required file (although the tutorial said only 3 files required).</div><div class=""><br class=""></div><div class="">Thanks a lot!</div><div class=""><br class=""></div><div class="">Ran</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: "PingFang SC";" class=""><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">setting up GFF3 output and fasta chunks</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">parseTagData: ID field not to EMBL spec "SNAP-OL2 repeatmasker; DNA; ???; BP.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">" from DE RepbaseID: SNAP-OL2XX</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9); min-height: 20px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> at /usr/local/apps/maker/v2.31.10/exe/RepeatMasker/RepeatMasker line 7611.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing repeat masking</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">running repeat masker.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#--------- command -------------#</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Widget::RepeatMasker:</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">cd /tmp/maker_joy_Oe; /usr/local/apps/maker/v2.31.10/exe/RepeatMasker/RepeatMasker /gpfs_common/share03/bonelllin/rzhang12/maker1/f2.renamed.maker.output/f2.renamed_datastore/04/3F/bviridis90138//theVoid.bviridis90138/0/bviridis90138.0.all.rb -species all -dir /gpfs_common/share03/bonelllin/rzhang12/maker1/f2.renamed.maker.output/f2.renamed_datastore/04/3F/bviridis90138//theVoid.bviridis90138/0 -pa 1</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#-------------------------------#</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">parseTagData: ID field not to EMBL spec "SNAP-OL2 repeatmasker; DNA; ???; BP.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">" from DE RepbaseID: SNAP-OL2XX</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9); min-height: 20px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> at /usr/local/apps/maker/v2.31.10/exe/RepeatMasker/RepeatMasker line 7611.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: RepeatMasker failed</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">--> rank=12, hostname=n3i4-13</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Failed while doing repeat masking</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Chunk failed at level:0, tier_type:1</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">FAILED CONTIG:bviridis90124</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9); min-height: 20px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Chunk failed at level:2, tier_type:0</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">FAILED CONTIG:bviridis90124</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9); min-height: 20px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">parseTagData: ID field not to EMBL spec "SNAP-OL2 repeatmasker; DNA; ???; BP.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">" from DE RepbaseID: SNAP-OL2XX</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9); min-height: 20px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> at /usr/local/apps/maker/v2.31.10/exe/RepeatMasker/RepeatMasker line 7611.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">parseTagData: ID field not to EMBL spec "SNAP-OL2 repeatmasker; DNA; ???; BP.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Andale Mono"; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">" from DE RepbaseID: SNAP-OL2XX</span></div><div class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><br class=""></span></div></div></div></body></html>