<div dir="ltr"><div class="gmail_default" style="font-family:georgia,serif"><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px">Hi,</p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px">I am trying to run a second round of Maker annotation job with a SNAP trained file. However, when I try to pass <code class="gmail-language-bash" style="box-sizing:inherit;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;font-size:1em;color:black;background:rgb(245,242,240);word-spacing:normal;word-break:normal;line-height:1.5;padding:0.1em;border-radius:0.3em">maker_gff<span class="gmail-token gmail-operator" style="box-sizing:inherit;color:rgb(154,110,58);background:rgba(255,255,255,0.5)">=</span>maker.all.gff.file.from.the.first.round.gff</code>. I get <code class="gmail-language-bash" style="box-sizing:inherit;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;font-size:1em;color:black;background:rgb(245,242,240);word-spacing:normal;word-break:normal;line-height:1.5;padding:0.1em;border-radius:0.3em">Non-unique top level ID</code> errors for all the scaffolds.</p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px"><code class="gmail-language-bash" style="box-sizing:inherit;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;font-size:1em;color:black;background:rgb(245,242,240);word-spacing:normal;word-break:normal;line-height:1.5;padding:0.1em;border-radius:0.3em">maker_round_1_master_datastore_index.log</code> shows failed reports for all the scaffolds.</p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px">I tried <code class="gmail-language-bash" style="box-sizing:inherit;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;font-size:1em;color:black;background:rgb(245,242,240);word-spacing:normal;word-break:normal;line-height:1.5;padding:0.1em;border-radius:0.3em">gff3_merge</code> with and without <code class="gmail-language-bash" style="box-sizing:inherit;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;font-size:1em;color:black;background:rgb(245,242,240);word-spacing:normal;word-break:normal;line-height:1.5;padding:0.1em;border-radius:0.3em">-l</code> flag, both <code class="gmail-language-bash" style="box-sizing:inherit;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;font-size:1em;color:black;background:rgb(245,242,240);word-spacing:normal;word-break:normal;line-height:1.5;padding:0.1em;border-radius:0.3em">gff3</code> files ended up giving the same error. I also tried <code class="gmail-language-bash" style="box-sizing:inherit;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;font-size:1em;color:black;background:rgb(245,242,240);word-spacing:normal;word-break:normal;line-height:1.5;padding:0.1em;border-radius:0.3em"><a href="http://gaas_maker_merge_outputs_from_datastore.pl">gaas_maker_merge_outputs_from_datastore.pl</a></code> and used <code class="gmail-language-bash" style="box-sizing:inherit;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;font-size:1em;color:black;background:rgb(245,242,240);word-spacing:normal;word-break:normal;line-height:1.5;padding:0.1em;border-radius:0.3em">maker_mix.gff</code> file for <code class="gmail-language-bash" style="box-sizing:inherit;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;font-size:1em;color:black;background:rgb(245,242,240);word-spacing:normal;word-break:normal;line-height:1.5;padding:0.1em;border-radius:0.3em">maker_gff</code>. It again fails with the same error.</p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px">When I grep non-unique id. It shows two hits one in `match` and the other in `match_part`.</p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px">I saw some tutorials not passing <code class="gmail-language-bash" style="box-sizing:inherit;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;font-size:1em;color:black;background:rgb(245,242,240);word-spacing:normal;word-break:normal;line-height:1.5;padding:0.1em;border-radius:0.3em">maker_gff</code> on the second round of the maker. But when I do that number of gene models decreases.</p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px">I have posted my question in Biostar (<a href="https://www.biostars.org/p/9506971/">https://www.biostars.org/p/9506971/</a>), with the maker_opts.ctl and error messages.</p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px">Can someone help me, please?</p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px">Thank you,</p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px">Upendra</p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px"><br></p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px"><br></p></div></div>