<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks, Carson, for these helpful hints.<div><br></div><div>(Separately, the other code did not work again on our cluster. Have been so swamped -- I'll get to the write-up next week. Have been using the 2.25beta binary and that works OK).</div><div><br></div><div>Best,</div><div>Bob</div><div><br><div><div>On Jun 3, 2013, at 9:04 AM, Carson Holt wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div 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>I don't have any specific advice, but In general I always set blast_depth parameters in the maker_bopts file to 20 or 30 (faster runtimes). Also max_dna_len can be set to 2x higher if you have sufficient memory (3-4 Gb per cpu as opposed to 1-2 Gb that are assumed with the default).</div><div><br></div><div>Other than that split_hit, pred_flank, and single_exon are the only ones I might change around. You sort of have to run on a few large contigs before deciding what to do with these parameters.</div><div><br></div><div>split_hit --> set max intron size for alignments</div><div>pred_flank --> affects clustering for gene dense organisms</div><div>single_exon --> leave off unless you expect a lot of singel exon genes.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> "Freeman, Robert M." <<a href="mailto:Bob_Freeman@hms.harvard.edu">Bob_Freeman@hms.harvard.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, 23 May, 2013 4:17 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Advice on params for ciliates<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear MAKER community,<div><br></div><div>Am embarking on updating models for a ciliate (taxa Ciliophora) and was wondering if folks had recommendations for MAKER parameters. </div><div><br></div><div>Thanks,</div><div>Bob</div><div><div><br class="Apple-interchange-newline"></div><br></div></div></div>_______________________________________________
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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></span></span><br class="Apple-interchange-newline">
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