<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Emmanuel, I think this script is expecting the file “uniprot_sprot.fasta” downloaded from the uniprot download page at <font color="#4787ff" class=""><u class=""><a href="http://www.uniprot.org/downloads#uniprotkblink" class="">http://www.uniprot.org/downloads#uniprotkblink</a></u></font><div class="">The fasta headers in this file are different from the fasta header that the file you used has: </div><div class=""><div style="margin: 0px; font-size: 11px; font-family: Menlo;" class="">>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;" class=""><br class=""></div><div style="margin: 0px;" class="">Let us know if that helps, </div><div style="margin: 0px;" class="">Daniel</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;" class=""><br class=""></div><div><blockquote type="cite" class=""><div class="">On Oct 2, 2017, at 1:03 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class="">Hello,<div class="">I intend to rename genes for Genebank submission</div><div class=""><br class=""></div><div class="">I downloaded swissprot.fa from NCBI and used blast MAKER generated file to swissprot. </div><div class=""><br class=""></div><div class="">the output of BLAST RESULT looks like this</div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">snap_masked-contig_8151-processed-gene-0.8-mRNA-1 P10978.1 49.315 73 37 0 43 115 874 946 2.61e-14 71.6</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">I attempted to run maker_funtional_gff using the swissprot.fa downloaded and the blastp result</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">I got the following result</span></div></div><div class=""><br class=""><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 2897906.</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 2897906.</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin; AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP; AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName: Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1; Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 1608599.</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 1608599.</span></div><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">
</span></p><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">What can I do?</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class=""><div class="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Emmanuel-5FNnadi_publications&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=7rmmgamH7FxikQu8KYDcWQ&m=msPeT4AvwkrDUCIhCkT2pdBnv3544Aw7GH4-1EaBLTI&s=xZn3vRB6bh2Dmlo_j8z7oR65G_I__AaOd8cUEs1TIqA&e=" target="_blank" class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div>
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