[maker-devel] Maker failing

[Fields, Christopher J]

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> on behalf of "Boyher, Adam" <ABoyher at danforthcenter.org>
Date: Wednesday, January 15, 2020 at 7:57 PM
To: "maker-devel at yandell-lab.org" <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
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

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