<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, can you send the command that produced the error? If you need to remove certain scaffolds or contigs from a gff3 file, you can use grep to to filter out certain scaffolds like this “grep -v “scaffold_name” gff3_file”. <div class=""><br class=""></div><div class="">~Daniel<br class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 26, 2017, at 5:34 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello,<div class=""><br class=""></div><div class="">I need to remove sequences from my GFF file can someone help me with command line for such removal</div><div class=""><br class=""></div><div class=""><div class="">ERROR: valid [SEQ_FEAT.FeatureBeginsOrEndsInGap] Feature begins or ends in gap starting at 17625 FEATURE: Gene: CR513_57782 <46071> [lcl|contig_14719:17653-17724] [lcl|contig_14719: delta, dna len= 17790]</div><div class="">ERROR: valid [SEQ_INST.ShortSeq] Sequence only 2 residues BIOSEQ: gnl|aceprd|CR513_62412: raw, aa len= 2</div><div class=""><br class=""></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://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div>
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