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

[Carson Holt]

My first thought is that one of your entries has a header and no sequence. Try this command with the fasta you are using —>

fasta_tool file.fasta --length | sort -nrk2

fasta_tool comes with maker. That command will report empty fasta entries at the bottom of the list with length 0.

Alternatively, MAKER accesses the input assembly using BioPerl. Update your BioPerl to the latest CPAN version (do not use BioPerl-live, as it will be less stable). Also BioPerl is using BerkleyDB for indexing, so if you are using a Perl that is not the system Perl (i.e. /usr/bin/perl), then it was lik,ly compiled on the machine you are using and could have been compiled without BerkleyDB support.

—Carson



> On Nov 14, 2017, at 5:15 AM, lahcen campbell <lahcencampbell at gmail.com> wrote:
> 
> 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 <mailto:lahcencampbell at gmail.com>                        <
> > https://www.ebi.ac.uk/about/people/lahcen-campbell <https://www.ebi.ac.uk/about/people/lahcen-campbell> <
> ==========================================
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