[maker-devel] ERROR: Failed while processing all repeats

[Carson Holt]

Sorry for the slow reply.  This issue gat lost.  It was caused by RepeatMasker reporting invalid coordinate for one of it’s results. Make sure to install the most recent MAKER release. It knows how to fix and ignore these odd results.

—Carson


> On Mar 18, 2021, at 6:58 PM, Inf Bio <bioinf49 at gmail.com> wrote:
> 
> Dear Developers,
> 
> I've researched all available forums and tried to resolve this recurring error in maker: 
> 
> processing all repeats
> in cluster::shadow_cluster...
> Died at /home/user/bin/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=19, hostname=m30g4
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> 
> So far, I have tried: reformatting my gff file including purify script from Carson, Daren Card's script, and agat; uninstalled and reinstalled ncbi-blast+ and updated path; reinstated RMBlast path in repeatmasker; changed max_dna_length to 300000; set clean_try=1; replaced RepeatMasker.pm.
> 
> However, none of the above helped get rid of the issue. I cannot see what is wrong with my gff. Can you please help?
> 
> thank you.
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