[maker-devel] Unwarranted error: Skipping the contig because it is too short

[lahcen campbell]

Hi MAKER community,

I was hoping someone could help me. I have a very unusual error with two
different versions of maker I have tested so far. This error shouldn't be
happening but it occurs time and again no matter what I try. I have tried
using 2.31.6_mpich3_icc and 2.31_mpich3

Note that version 2.31.6_mpich3_icc is one I have used countless times and
produced final MAKER annotations without issue. So its not that this
version has issues to date.

Basically, this is a brand new MAKER analysis, I am only trying to train
SNAP in this first round. I am following the MakerTutorial as documented
this time around and I can't get past the initial SNAP train stage.

I have a single genome file with, 10 Long scaffolds making up just under
11MB (subsampled from my original full length assembly) of sequence data in
which to train SNAP. The fasta file is not corrupted, and has been
generated in various ways in order to test formatting issues etc.

I have only edited the maker_opts file and changed:

*genome=*
*protein=*
*protein2genome=1*

But see attached my maker CTL files.

The error consistently returned to me:

*Skipping the contig because it is too short!!*
*SeqID: contig_WHATEVER*
*Length: 0*

*The sequences are no where near too short. This was verified independently
outside maker to be sure. *

*The headers are as follows:*

>tig00000458 len=2889428 reads=4143 covStat=1793.77 gappedBases=no
class=contig suggestRepeat=no suggestCircular=no
>tig00000159 len=3515005 reads=5100 covStat=2143.94 gappedBases=no
class=contig suggestRepeat=no suggestCircular=no
>tig00006117 len=1009519 reads=1168 covStat=804.93 gappedBases=no
class=contig suggestRepeat=no suggestCircular=no
>tig00000419 len=2633986 reads=3938 covStat=1519.93 gappedBases=no
class=contig suggestRepeat=no suggestCircular=no
>tig00027677 len=108573 reads=86 covStat=86.05 gappedBases=no class=contig
suggestRepeat=no suggestCircular=no
>tig00021790 len=202251 reads=158 covStat=184.12 gappedBases=no
class=contig suggestRepeat=no suggestCircular=no
>tig00316948 len=280333 reads=237 covStat=253.23 gappedBases=no
class=contig suggestRepeat=no suggestCircular=no
>tig00019606 len=149709 reads=82 covStat=150.02 gappedBases=no class=contig
suggestRepeat=no suggestCircular=no
>tig00023852 len=189461 reads=115 covStat=192.28 gappedBases=no
class=contig suggestRepeat=no suggestCircular=no
>tig00316994 len=19742 reads=1 covStat=0.00 gappedBases=no class=contig
suggestRepeat=no suggestCircular=no

I have just about given up, I have no idea why its happening it makes zero
sense.

Any help or information as to why this might be happening would be amazing.

Thank you in advance.
Lahcen

-- 
==========================================
> Dr. Lahcen Campbell                                                  <
> Contact: lahcencampbell at gmail.com                        <
> https://www.ebi.ac.uk/about/people/lahcen-campbell <
==========================================
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20171114/f44b8bb0/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: maker_bopts.ctl
Type: application/octet-stream
Size: 1413 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20171114/f44b8bb0/attachment-0006.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: maker_exe.ctl
Type: application/octet-stream
Size: 1512 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20171114/f44b8bb0/attachment-0007.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: maker_opts.ctl
Type: application/octet-stream
Size: 5560 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20171114/f44b8bb0/attachment-0008.obj>