<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">I got the same error as previously mentioned by Greer Dolby the 15th of June.</div><div class="">I share my experience hopping it could help to catch the problem.</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">.processing 0 of 5</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ...processing 1 of 5</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ...processing 2 of 5</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ...processing 3 of 5</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ...processing 4 of 5</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ...processing 0 of 6</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ...processing 1 of 6</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ...processing 2 of 6</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ...processing 3 of 6</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ...processing 4 of 6</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ...processing 5 of 6</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">adding statistics to annotations</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Calculating annotation quality statistics</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">choosing best annotation set</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Choosing best annotations</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Died at /sw/bioinfo/maker/3.01.02-beta-OMPI-perl5.16/bin/../lib/maker/auto_annotator.pm line 1774.</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">--> rank=36, hostname=bnode-06</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Failed while choosing best annotation set</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Chunk failed at level:4, tier_type:4</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(34, 79, 188);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">FAILED CONTIG:@000261F|arrow|arrow</span></div></div><br class=""><div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">I’m using:</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">- MAKER 3.01.02-beta</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">- openmpi 2.1.2</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">- perl 5.16.3</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">- BioPerl 1.6.922</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">- Exonerate 2.4</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">- blast+ 2.7.1</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">- evm 1.1.1</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">- genemark 4.3</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">- augustus 2.7</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">- repeat masker 4.0.3</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""></div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">As externaI data I use proteins in fasta format, transcriptomes in fasta format and transcriptomes in gff format.</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">I have first run MAKER with est2genome and protein2genome set to 1 and single_exon=1 (important for the bug it seems). => it has worked fine</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Then I have run the same data with est2genome and protein2genome set to 0 and genemark, snap, augustus and evm activated and still single_exon=1 => it has worked fine.</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">I wanted to give a last try with the same parameters as the previous run but put single_exon=0 => 2 contigs crash on the 6000 contigs my assembly has</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""></div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">I have extracted the sequence and relaunched MAKER apart it in a fresh folder. I have exactly the same error.</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""></div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Best regards,</div><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class="">Jacques</div></div></div>
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