<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Is there any way to re-try maker pipeline on just Failed scaffolds separately?</div><div><br></div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div>Yes. The failed contig fasta will be in the maker.output subdirectory for that contig. Alternatively use the fasta_tool script to extract them from the genome file. You can then run them in a separate directory, or use the '-base' command line flag to force it to use the base name of the current results directory. Use the –g option to override the genome file without having to edit the control files</div><div><br></div><div>Example:</div><div><br></div><div>maker -g failed.fasta –base maize_assemby</div><div><br></div><div>Output will end up here --> maize_assemby.maker.output</div></blockquote><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><div lang="KO" link="blue" vlink="purple"><div class="WordSection1"><div><p class="MsoNormal"><span lang="EN-US">And do I have to manually erase for the failed directories named as ../theVoid.scaffold_#/?</span></p></div></div></div></div></span><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div>No. You can let MAKER just retry them as is (let maker handle what to delete and keep) or set clean_try=1 to force full deletion before rerunning</div></blockquote><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><div lang="KO" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p><div><p class="MsoNormal"><span lang="EN-US">And how can I track down the reason why only those 20 out of around 3000 scaffolds?</span></p></div></div></div></div></span><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div>Search for the tag "ERROR" in the standard output of your run. What MAKER version are you using? I can take a look at the STDERR as wel if you want. If it's too big for e-mail, you can share it via dropbox.</div></blockquote><div><br></div><div><br></div><div><br></div><div>Thanks,</div><div>Carson</div></body></html>