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Hello,<br>
<br>
I'm trying to use the MAKER pipeline to calculate AED scores for the
gene models coming out of our annotation pipeline (EVidence
Modeler). We then want to compare these computed AED scores with
those computed for the gene models coming out of the MAKER2
pipeline.<br>
<br>
For this purpose, I configured the maker_opts.ctl file like so:<br>
1) Specify gff file coming from our annotation pipeline using
`model_gff` param <br>
2) Specify gff file containing est2genome results (computed using
MAKER2) using the `est_gff` param<br>
3) Specify gff file containing protein2genome results (computed
using MAKER2) using the `protein_gff` param<br>
4) Specify the genome fasta sequence file using the `genome` param<br>
<br>
I recently configured MAKER 2.27b to work using MPI and I tried
launching one contig (chromosome) on a compute node spawning 12
processes like so:<br>
<big><tt>mpiexec -n 12 maker -R -TMP /tmp/maker maker_opts.ctl
maker_bopts.ctl maker_exe.ctl 2>&1 | tee maker.err</tt></big><br>
<br>
Side note: Without MPI, it works fine but takes very very long to
complete running on one chromosome (since it is going through the
chunks serially).<br>
<br>
On inspecting the `maker.err` file, I see server error messages that
say `DBD::SQLite::db do failed: database is locked`. On referring to
a previous email thread on the `maker-devel` mailing list, I see
that Carson had replied to the person with a similar issue asking
them to check if the working directory and TMP directory are being
mounted on an NFS filesystem because this is a potential problem
with SQLite databases.<br>
<br>
Based on that suggestion, I switched the TMP directory to use a
local filesytem but the working directory is still NFS mounted.
Despite that, I still get this error. The previous email thread had
no resolution for this issue. My question is, should the working
directory be local as well? I see that despite setting the `TMP`
variable, the SQLite DB is getting created in the working directory.<br>
<br>
What might be the issue?<br>
<br>
Also, apart from this one error, I notice another error:<br>
<big><tt>ERROR: Non-unique top level ID for chr5:hit:1454:4_0<br>
While this is technically legal in GFF3, it usually<br>
indicates a poorly fomatted GFF3 file (perhaps you<br>
tried to merge two GFF3 files without accounting for<br>
unique IDs). MAKER will not handle these correctly.</tt></big><br>
<br>
On inspecting the input GFF file (protein2genome), I see that this
ID is never repeated. So I have no idea whats going on here either.
Any suggestions?<br>
<br>
Below is my `maker.err` file from the run. (Dropbox link)<br>
<br>
Thank you very much.<br>
Best,<br>
<br>
Vivek<br>
<br>
--<br>
Vivek Krishnakumar<br>
<a class="moz-txt-link-abbreviated" href="mailto:vkrishnakumar@jcvi.org">vkrishnakumar@jcvi.org</a><br>
<br>
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