[maker-devel] Maker failing

[Carson Holt]

The directory /scratch/dir_60712 may not be true local disk. It may be network mounted space. The IO characteristics of network disk can create errors for files that are written and read immediately afterward.  Let TMP= in the maker_opts.ctl file be the default of /tmp.

—Carson



> On Jan 16, 2020, at 8:42 AM, Boyher, Adam <ABoyher at danforthcenter.org> wrote:
> 
> Genome size is about 1.5Gbp and transcripts are around 22Gbp 😳. I know that's huge. I used hisat to align the rnaseq, stringtie, then bedtools to extract the sequence so I could use it as est fasta.
> 
> Get Outlook for Android <https://aka.ms/ghei36>
> From: Fields, Christopher J <cjfields at illinois.edu <mailto:cjfields at illinois.edu>>
> Sent: Thursday, January 16, 2020 9:03:46 AM
> To: Boyher, Adam <ABoyher at danforthcenter.org <mailto:ABoyher at danforthcenter.org>>; maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: Re: [maker-devel] Maker failing
>  
> It’s been a few years but I have seen this when one of the MAKER job chunks fails, the chance increases with genome and input data size.  I recall it being worse when using a network file system at that time.
>  
> chris
>  
> From: maker-devel <maker-devel-bounces at yandell-lab.org <mailto:maker-devel-bounces at yandell-lab.org>> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org <mailto:ABoyher at danforthcenter.org>>
> Date: Wednesday, January 15, 2020 at 7:57 PM
> To: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: [maker-devel] Maker failing
>  
> Hi
> I’ve been having this issue for a few weeks with Maker. I thought it was just a memory issue, I’ve recently started annotating a larger genome with more evidence. But I’m not sure that’s the issue anymore. The most recent run yielded this error:
>  
> ERROR: The file /scratch/dir_60712/maker_h8TIEf/12/Chromosome10_0.7125796-7129044.RNAseqTISSUE_Chromosome06_0%3A14710146-14710774.e.exonerate appears to be incomplete
> MAKER will need to delete the file, before trying again
>  
> --> rank=12, hostname=pacifica.datasci.danforthcenter.org <http://pacifica.datasci.danforthcenter.org/>
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:3
> FAILED CONTIG:Chromosome10_0
>  
>  
> Any idea what could cause that?
> 
> Adam
>  
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>  
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