<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hello !<div><br></div><div>After running a genome containing 7,752 scaffolds, I have some differences in outputs.</div><div>For some I have less files in the datastore.</div><div>For instance, for one, I have only :</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE337098%2E1.gff</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE337098%2E1.maker.augustus.proteins.fasta</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE337098%2E1.maker.augustus.transcripts.fasta</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">run.log</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(83, 48, 225); background-color: rgb(0, 0, 0);">theVoid.KE337098.1</div><div><br></div><div>And others have more:</div><div><span style="background-color: rgb(0, 0, 0); color: rgb(41, 249, 20); font-family: 'Andale Mono';">KE332545%2E1.gff</span></div><div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE332545%2E1.maker.augustus_masked.proteins.fasta</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE332545%2E1.maker.augustus_masked.transcripts.fasta</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE332545%2E1.maker.augustus.proteins.fasta</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE332545%2E1.maker.augustus.transcripts.fasta</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE332545%2E1.maker.non_overlapping_ab_initio.proteins.fasta</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE332545%2E1.maker.non_overlapping_ab_initio.transcripts.fasta</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE332545%2E1.maker.proteins.fasta</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE332545%2E1.maker.transcripts.fasta</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE332545%2E1.maker.trnascan.transcripts.fasta</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">run.log</div></div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);"><div style="margin: 0px; color: rgb(83, 48, 225);">theVoid.KE332545.1</div></div><div><br></div><div>I checked that for these two scaffolds, it is written FINISHED in the output.</div><div>Do we agree that as long as a scaffold is written FINISHED it is OK ?</div><div>And that the process won’t start again if I relaunch Maker in the same directory ?</div><div>I am asking this second question as I had to relaunch several times…</div><div><br></div><div>Also, I have something weird for some scaffolds. It has failed but the FAILED is written in column 2 of the output.</div><div>For instance if I grep a single scaffold:</div><div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: rgb(195, 55, 32);">7098</span>.1<span class="Apple-tab-span" style="white-space: pre;"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>Pdac_ref2013s_datastore/23/51/KE33<span style="color: #c33720">7098</span>.1/<span class="Apple-tab-span" style="white-space:pre"> </span>STARTED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>Pdac_ref2013s_datastore/23/51/KE33<span style="color: #c33720">7098</span>.1/<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>FAILED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>Pdac_ref2013s_datastore/23/51/KE33<span style="color: #c33720">7098</span>.1/<span class="Apple-tab-span" style="white-space:pre"> </span>RETRY</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">KE33<span style="color: #c33720">7098</span>.1<span class="Apple-tab-span" style="white-space:pre"> </span>Pdac_ref2013s_datastore/23/51/KE33<span style="color: #c33720">7098</span>.1/<span class="Apple-tab-span" style="white-space:pre"> </span>FINISHED</div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(52, 189, 38); background-color: rgb(0, 0, 0);"><br></div></div><div><br></div><div>Is this problematic at some point or since it’s also written FINISHED, I should not worry ?</div><div><br></div><div>Thanks a lot,</div><div><br></div><div>Muriel</div><div><br></div></body></html>