<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Greetings,<div><br></div><div>Am using MAKER 2.27b to annotate a ciliate genome and am finding that my log files are growing to GB sizes. When looking more carefully, an error seems to be occurring around the Repeatmasker stage:</div><div><br></div><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">....</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">Now starting the contig!!</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">--</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;"><br></span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">setting up GFF3 output and fasta chunks</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">doing repeat masking</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">doing blastx repeats</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">doing blastx of proteins</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">doing blastx of proteins</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">doing blastx of proteins</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">doing blastx repeats</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">collecting blastx repeatmasking</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">processing all repeats</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">ERROR: Can't open seq file: /files/.retain-snapshots.d14d-w60d/SysBio/klab_genome/maker/stentor/run_current_r3/soapPrice1.cycle7.maker.output/soapPrice1.cycle7_datastore/03/EF/contig_157//theVoid.contig_157/query.masked.gff.seq</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">No such file or directory</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;"><br></span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;"> at /groups/acornworm/opt/maker-2.27-beta/bin/../lib/Dumper/GFF/GFFV3.pm line 182</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;"> Dumper::GFF::GFFV3::finalize('Dumper::GFF::GFFV3=HASH(0x50547f8)') called at /groups/acornworm/opt/maker-2.27-beta/bin/../lib/Process/MpiChunk.pm line 691</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;"> Process::MpiChunk::__ANON__() called at /groups/acornworm/opt/maker-2.27-beta/bin/../lib/Error.pm line 415</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;"> eval {...} called at /groups/acornworm/opt/maker-2.27-beta/bin/../lib/Error.pm line 407</span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;"> Error::subs::try('CODE(0x5b859c0)', 'HASH(0x11ea63f0)') called at /groups/acornworm/opt/maker-2.27-beta/bin/../lib</span></font></div></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="font-size: 11px;">...</span></font></div></blockquote><div><br></div><div>I don't seem to have this problem when I fall back to the 2.25b version (though I start having major DBD:SQLite issues).</div><div><br></div>I'm doing this on a cluster, running this under MPI with 50 cores.<div><br></div><div>Any help/suggestions would be appreciated!</div><div><br></div><div>-Bob</div><div><br><div><div apple-content-edited="true">
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-webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; ">-----------------------------------------------------</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Bob Freeman, Ph.D.</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Acorn Worm Informatics, Kirschner lab</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dept of Systems Biology, Alpert 524</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Harvard Medical School</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">200 Longwood Avenue</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Boston, MA 02115</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">617/432.2294, vox</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><span class="Apple-style-span" style="font-size: medium; "><div><div><div><div><div><div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br><div style="font-style: normal; ">"Sorry I'm late. Oh, God, that sounded insincere. I'm late."</div><div><span class="Apple-tab-span" style="font-style: normal; white-space: pre; "> </span>-- Karen Walker, from<span class="Apple-converted-space"> </span><i>Will and Grace</i></div><div style="font-style: normal; "><br></div></span></font></div></div></div></div></div></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div><br class="Apple-interchange-newline">
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