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I just ran Maker on my 75,507 unitig database. The maker_opts.ctl file included EST Evidence in the form of a large transcript rna file from Arabidopsis thaliana (GenBank) for est=, and protein= files from Arabidopsis thaliana and a uniprot file from a closely
related plant to my organism. All contigs started and finished. Looking at the SLURM output some of them ran the #Widget:: RepeatMasker only.
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<div class="">Other contigs (e.g. tig00000004) ran 111 pages of RepeatMasker, blastx repeats, formater, running blast search, blastx, setting up GFF3 output and fast chunks, formatting database, etc. on the Arabidopsis rna file, then on the two protein files.</div>
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<div class="">However, when I look at the location of that particular contig <span style="caret-color: rgba(0, 0, 0, 0); color: rgb(240, 240, 240); font-family: "DejaVu Sans Mono", "Noto Sans Mono", "Everson Mono", FreeMono, Menlo, Terminal, monospace; font-size: 15px; white-space: pre; background-color: rgb(16, 16, 16);" class="">
ptero.unitigs_datastore/C3/F2/tig00000004/</span> in the _master_datastor_index.log file</div>
<div class="">I get only this:</div>
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<div class=""><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height); caret-color: rgba(0, 0, 0, 0); color: rgb(240, 240, 240); font-family: "DejaVu Sans Mono", "Noto Sans Mono", "Everson Mono", FreeMono, Menlo, Terminal, monospace; font-size: 15px; white-space: pre;" class=""><span style="color: rgb(52, 101, 164);" class="">..</span><span style="color: rgb(6, 152, 154);" class="">/</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height); caret-color: rgba(0, 0, 0, 0); color: rgb(240, 240, 240); font-family: "DejaVu Sans Mono", "Noto Sans Mono", "Everson Mono", FreeMono, Menlo, Terminal, monospace; font-size: 15px; white-space: pre;" class=""><span style="color: rgb(52, 101, 164);" class="">.</span><span style="color: rgb(6, 152, 154);" class="">/</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height); caret-color: rgba(0, 0, 0, 0); color: rgb(240, 240, 240); font-family: "DejaVu Sans Mono", "Noto Sans Mono", "Everson Mono", FreeMono, Menlo, Terminal, monospace; font-size: 15px; white-space: pre;" class=""><span style="color: rgb(52, 101, 164);" class="">theVoid.tig00000004</span><span style="color: rgb(6, 152, 154);" class="">/</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height); caret-color: rgba(0, 0, 0, 0); font-family: "DejaVu Sans Mono", "Noto Sans Mono", "Everson Mono", FreeMono, Menlo, Terminal, monospace; font-size: 15px; white-space: pre;" class="">run.log</x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height); caret-color: rgba(0, 0, 0, 0); font-family: "DejaVu Sans Mono", "Noto Sans Mono", "Everson Mono", FreeMono, Menlo, Terminal, monospace; font-size: 15px; white-space: pre;" class="">tig00000004.gff</x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height); caret-color: rgba(0, 0, 0, 0); font-family: "DejaVu Sans Mono", "Noto Sans Mono", "Everson Mono", FreeMono, Menlo, Terminal, monospace; font-size: 15px; white-space: pre;" class="">.swp</x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height); caret-color: rgba(0, 0, 0, 0); font-family: "DejaVu Sans Mono", "Noto Sans Mono", "Everson Mono", FreeMono, Menlo, Terminal, monospace; font-size: 15px; white-space: pre;" class=""><br class="">
</x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre; font-style: normal;" class="">There is
</span><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class="">no maker.proteins.fasta or maker.transcripts.fasta file.
</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class=""><br class="">
</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class="">When I look at the tig00000004.gff file, it is empty.</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class=""><br class="">
</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class="">Am I even on the right track?</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class=""><br class="">
</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class="">Thanks for any help you can provide.</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class="">Sincerely,</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class="">Steve
Miller</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class="">Botany</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class="">University
of Wyoming</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class=""><br class="">
</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class=""><br class="">
</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class=""><br class="">
</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class=""><br class="">
</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class=""><br class="">
</span></x-row><x-row style="display: block; height: var(--hterm-charsize-height); line-height: var(--hterm-charsize-height);" class=""><span style="caret-color: rgba(0, 0, 0, 0); white-space: pre;" class=""><br class="">
</span></x-row></div>
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