<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="">The directory /scratch/dir_60712 may not be true local disk. It may be network mounted space. The IO characteristics of network disk can create errors for files that are written and read immediately afterward. Let TMP= in the maker_opts.ctl file be the default of /tmp.<div class=""><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 16, 2020, at 8:42 AM, Boyher, Adam <<a href="mailto:ABoyher@danforthcenter.org" class="">ABoyher@danforthcenter.org</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="auto" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(33, 33, 33); background-color: rgb(255, 255, 255); text-align: left;" class="">Genome size is about 1.5Gbp and transcripts are around 22Gbp 😳. I know that's huge. I used hisat to align the rnaseq, stringtie, then bedtools to extract the sequence so I could use it as est fasta.</div><div id="ms-outlook-mobile-signature" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><div class=""><br class=""></div>Get<span class="Apple-converted-space"> </span><a href="https://aka.ms/ghei36" style="color: blue; text-decoration: underline;" class="">Outlook for Android</a></div><hr tabindex="-1" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; display: inline-block; width: 1571.90625px;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" style="color: blue; text-decoration: underline;" class="">cjfields@illinois.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, January 16, 2020 9:03:46 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Boyher, Adam <<a href="mailto:ABoyher@danforthcenter.org" style="color: blue; text-decoration: underline;" class="">ABoyher@danforthcenter.org</a>>;<span class="Apple-converted-space"> </span><a href="mailto:maker-devel@yandell-lab.org" style="color: blue; text-decoration: underline;" class="">maker-devel@yandell-lab.org</a><span class="Apple-converted-space"> </span><<a href="mailto:maker-devel@yandell-lab.org" style="color: blue; text-decoration: underline;" class="">maker-devel@yandell-lab.org</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [maker-devel] Maker failing</font><div class=""> </div></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><div class="WordSection1"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">It’s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size. I recall it being worse when using a network file system at that time.</div><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">chris</div><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org" style="color: blue; text-decoration: underline;" class="">maker-devel-bounces@yandell-lab.org</a>> on behalf of "Boyher, Adam" <<a href="mailto:ABoyher@danforthcenter.org" style="color: blue; text-decoration: underline;" class="">ABoyher@danforthcenter.org</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Wednesday, January 15, 2020 at 7:57 PM<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b>"<a href="mailto:maker-devel@yandell-lab.org" style="color: blue; text-decoration: underline;" class="">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" style="color: blue; text-decoration: underline;" class="">maker-devel@yandell-lab.org</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>[maker-devel] Maker failing</span></div></div><div class=""><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I’ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I’ve recently started annotating a larger genome with more evidence. But I’m not sure that’s the issue anymore. The most recent run yielded this error:</div><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">MAKER will need to delete the file, before trying again</div><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">--> rank=12, hostname=<a href="http://pacifica.datasci.danforthcenter.org/" style="color: blue; text-decoration: underline;" class="">pacifica.datasci.danforthcenter.org</a></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">ERROR: Failed while polishig ESTs</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">ERROR: Chunk failed at level:2, tier_type:3</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">FAILED CONTIG:Chromosome10_0</div><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Any idea what could cause that?</div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class="">Adam</div><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Sent from<span class="Apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" style="color: blue; text-decoration: underline;" class="">Mail</a><span class="Apple-converted-space"> </span>for Windows 10</div><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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