[maker-devel] Fasta index error

[Fields, Christopher J]

Victor,

Can you post which version of MAKER you are using?

chris


On Jul 7, 2016, at 6:25 AM, Victor Rossier <Victor.Rossier at unil.ch<mailto:Victor.Rossier at unil.ch>> wrote:

Thanks for the quick replies,

It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'.

I renamed all transcripts and maker finished correctly!

Thanks again,
Victor Rossier

________________________________
De : Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>>
Envoyé : mercredi 6 juillet 2016 14:16
À : Carson Holt
Cc : Victor Rossier; maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
Objet : Re: [maker-devel] Fasta index error

I’ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case.

chris

On Jul 5, 2016, at 9:29 AM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:

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<mailto: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<https://urldefense.proofpoint.com/v2/url?u=http-3A__dee-2Dserv04.vital-2Dit.ch_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=IMqKG5fcHs_DVo3tdSTcbqMWVKDw9ntAr8RMBGD45_M&s=KvnplP4Ch4nKxsCIW-K3rDj6OLpTNh1ND6cgWYs24U8&e=>
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
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