[maker-devel] maker problem

[Carson Holt]

Separate out just that contig into a separate file and run it by itself.  You may also want to rename the contig.  Don’t call it 0.  Having the name simply be a zero has the potential to cause any number of problems in MAKER or any of the programs MAKER uses because 0 all by itself means ‘false’ in most computer languages.  Try contig_0 instead. It looks like the first error may be the BioPerl indexer failing because the contig is named 0.

—Carson


> On Aug 30, 2015, at 2:52 AM, 尹传林 <yincl2013 at 126.com> wrote:
> 
> Hello,  
>  
> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I donot konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much.  
>  
> Here is a part of main error log:   
> WARNING: Cannot find >0, trying to re-index the fasta.  
> stop here:0  
> ERROR: Fasta index error  
>  at /disk/yinchuanlin/software/maker/maker/bin/../lib/GI.pm line 1622.  
>  GI::polish_exonerate(FastaChunk=HASH(0x7fe0263563b8), FastaSeq=HASH(0x3f7b280), 2988503, ">contig1", ARRAY(0x3d3ad80), ARRAY(0x3d17ed0), "/disk/yinchuanlin/01_pingguodue_project/02_OMIGA/09_maker_wor"..., "e", "/disk/yinchuanlin/software/maker/exonerate-2.2.0-x86_64/bin/e"..., ...) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiChunk.pm line 1986  
>  Process::MpiChunk::__ANON__() called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Error.pm line 415  
>  eval {...} called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Error.pm line 407  
>  Error::subs::try(CODE(0x3f381b8), HASH(0x3f62380)) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiChunk.pm line 4224  
>  Process::MpiChunk::_go(Process::MpiChunk=HASH(0x3e30020), "run", HASH(0x7fe026352410), 2, 3) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiChunk.pm line 341  
>  Process::MpiChunk::run(Process::MpiChunk=HASH(0x3e30020), 0) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiChunk.pm line 357  
>  Process::MpiChunk::run_all(Process::MpiChunk=HASH(0x3e30020), 0) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiTiers.pm line 287  
>  Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x3d43310), 0) called at /disk/yinchuanlin/software/maker/maker/bin/../lib/Process/MpiTiers.pm line 287  
>  Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x3f28b28), 0) called at /disk/yinchuanlin/software/maker/maker/bin/maker line 686  
> --> rank=NA, hostname=node7  
> ERROR: Failed while polishig ESTs  
> ERROR: Chunk failed at level:2, tier_type:3  
> FAILED CONTIG:contig1  
>  
> ERROR: Chunk failed at level:4, tier_type:0  
> FAILED CONTIG:contig1  
>  
> Thanks!  
>  
> Best regards,  
> Ian  
> Department of Entomology, College of Plant Protection, Nanjing Agricultural University   
> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China  
>  
>  
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