[maker-devel] Fasta index error
Carson Holt
carsonhh at gmail.com
Tue Jul 5 08:29:14 MDT 2016
You need to rename the contig. It is currently named 0
The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it’s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed.
You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference.
—Carson
> On Jul 4, 2016, at 9:38 AM, Victor Rossier <Victor.Rossier at unil.ch> wrote:
>
> Dear Maker,
>
> I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1.
>
> Here is the error I get:
>
> WARNING: Cannot find >0, trying to re-index the fasta.
> stop here:0
> ERROR: Fasta index error
> at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622.
> GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491
> Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415
> eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407
> Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224
> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341
> Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979
> --> rank=16, hostname=dee-serv04.vital-it.ch <http://dee-serv04.vital-it.ch/>
> ERROR: Failed while polishing alt-ESTs
> ERROR: Chunk failed at level:6, tier_type:3
> FAILED CONTIG:scaffold52256_cov106
>
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:scaffold52256_cov106
>
> Any thought how to solve this?
>
> Thanks in advance,
> Victor Rossier
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20160705/c6ee2df5/attachment-0003.html>
More information about the maker-devel
mailing list