<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;">Yes, the GFF3 file generated by maker is missing these ID. </span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;"><br data-mce-bogus="1"></span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;">The <span style="background: white;" data-mce-style="background: white;">master_datastore_index file indicate failed runs on the scaffolds</span> (scaffold_1710 and <span style="background: white;" data-mce-style="background: white;">scaffold_1734), w</span>hich could cause the error. </span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;"><br data-mce-bogus="1"></span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;">I have managed the problem by extracting the missing ID doing a "grep" into the gff3 file using AED and QI statistics and then replace missing ID into the proteinf fasta file like below:</span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;"> </span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;">% map_fasta_ids maker.all.map all.maker.proteins.fasta</span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;"> </span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;">WARNING: No mapping available for maker-scaffold_1710-augustus-gene-0.3-mRNA-1</span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;"> </span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;">% grep "maker-scaffold_1710-augustus-gene-0.3-mRNA-1" all.maker.proteins.fasta</span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;">>maker-scaffold_1710-augustus-gene-0.3-mRNA-1 protein AED:0.00 eAED:0.00 QI:50|1|1|1|0.66|0.75|4|142|117</span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;"> </span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;">% grep "<strong>_AED=0.00;_QI=50|1|1|1|0.66|0.75|4|142|117;_eAED=0.00</strong>" maker.gff</span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;"> </span></p><p style="margin: 0px; line-height: normal; background: white;" data-mce-style="margin: 0px; line-height: normal; background: white;"><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: black;">scaffold_1710 maker mRNA 120513 125092 . + . ID=AV_03422-RA;Parent=AV_03422;Name=AV_03422-RA;Alias=<strong>maker-scaffold_1710-augustus-gene-0.23-mRNA-1</strong>;<strong>_AED=0.00;_QI=50|1|1|1|0.66|0.75|4|142|117;_eAED=0.00</strong>;</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif';" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif';"> </span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif';" style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif';"># Then, Replace in the </span><span data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: black;" style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: black;">all.maker.proteins.fasta</span><span data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif';" style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif';"> "</span><span data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: black;" style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: black;">maker-scaffold_1710-augustus-gene-0.3-mRNA-1" by " <strong>maker-scaffold_1710-augustus-gene-0.23-mRNA-1</strong>"</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: black;" style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: black;"><br data-mce-bogus="1"></span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: black;" style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: black;">Best, </span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: black;" style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: black;">Amine</span></p></div><div><br></div><hr id="zwchr" data-marker="__DIVIDER__"><div data-marker="__HEADERS__"><b>De: </b>"chebbi mohamed amine" <mohamed.amine.chebbi@univ-poitiers.fr><br><b>À: </b>"Carson Holt" <carsonhh@gmail.com><br><b>Cc: </b>"Maker Mailing List" <maker-devel@yandell-lab.org><br><b>Envoyé: </b>Mardi 29 Novembre 2016 10:08:56<br><b>Objet: </b>Re: [maker-devel] map_fasta_ids : No mapping available...<br></div><div><br></div><div data-marker="__QUOTED_TEXT__"><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000;" data-mce-style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000;"><div>Yes, the GFF3 file genrated by maker is missing these ID. the <span style="color: #000000; font-family: monospace, Courier; font-size: 12.8px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;" data-mce-style="color: #000000; font-family: monospace, Courier; font-size: 12.8px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;">master_datastore_index file indicate failed runs on the scaffolds</span> (scaffold_1710 and <span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;"><span style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;" data-mce-style="color: #000000; font-family: arial, helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff; display: inline !important; float: none;">scaffold_1734), </span></span>Which could cause the error. </div><div>I have managed the problem by extracting the missing ID doing a grep in to AED and QI statistics</div><hr id="zwchr"><div><b>De: </b>"Carson Holt" <carsonhh@gmail.com><br><b>À: </b>"Mohamed Amine Chebbi" <mohamed.amine.chebbi@univ-poitiers.fr><br><b>Cc: </b>"Maker Mailing List" <maker-devel@yandell-lab.org><br><b>Envoyé: </b>Lundi 28 Novembre 2016 17:26:40<br><b>Objet: </b>Re: [maker-devel] map_fasta_ids : No mapping available...<br></div><br><div>The map file you run with is two columns (old_id and new_id). If the input file has IDs that do not match anything in the old_id column then it throws the warning. It means there is a mismatch between the map file being used and the fasta file. This can occur if you did downstream manipulation of the fasta file, are using the wrong fasta file, or if you used GFF3 as input to a maker step that as generated an ID mismatch.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote class=""><div class="">On Nov 24, 2016, at 2:45 PM, Mohamed Amine Chebbi <<a href="mailto:mohamed.amine.chebbi@univ-poitiers.fr" class="" target="_blank" data-mce-href="mailto:mohamed.amine.chebbi@univ-poitiers.fr">mohamed.amine.chebbi@univ-poitiers.fr</a>> wrote:</div><div class=""><div class=""><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;" class="" data-mce-style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"><div class="">Hello !</div><div class=""><br class=""></div><div class="">I'am attempting to rename genes of maker.proteins.fasta for Genebank submission using the map_fasta_ids script. It seems to work correctly for the major of gene models, except to those ones having the below warning message :</div><div class=""><br class=""></div><div class="">WARNING: No mapping available for maker-scaffold_1710-augustus-gene-0.3-mRNA-1</div><div class="">WARNING: No mapping available for maker-scaffold_1710-augustus-gene-0.0-mRNA-1<br class="">WARNING: No mapping available for maker-scaffold_1710-snap-gene-0.6-mRNA-1<br class="">WARNING: No mapping available for maker-scaffold_1710-augustus-gene-0.4-mRNA-1<br class="">WARNING: No mapping available for maker-scaffold_1734-augustus-gene-0.1-mRNA-1<br class="">WARNING: No mapping available for maker-scaffold_1734-augustus-gene-0.2-mRNA-1<br class="">WARNING: No mapping available for maker-scaffold_1734-augustus-gene-0.0-mRNA-1<br class="">WARNING: No mapping available for maker-scaffold_1734-augustus-gene-0.5-mRNA-1<br class="">WARNING: No mapping available for maker-scaffold_1734-augustus-gene-0.6-mRNA-1<br class="">WARNING: No mapping available for maker-scaffold_1734-snap-gene-0.15-mRNA-1<br class="">WARNING: No mapping available for maker-scaffold_1734-snap-gene-0.16-mRNA-1<br class=""></div><div class=""><br class=""></div><div class="">Looking into the maker.gff file, these gene names are missing and may be replaced by other ones which differ by the numbers following the gene predictor.</div><div class=""><br class=""></div><div class="">I wounder if you can explain me the reason of these warning message and how to resolve it.</div><div class=""><br class=""></div><div class="">Thank you ,</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Amine</div></div></div>_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="" target="_blank" data-mce-href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></div></div></div><br></div></div></body></html>