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From: | José Víctor Moreno Mayar |
Subject: | Re: [Bammds-users] ASD file error |
Date: | Sun, 7 Sep 2014 16:16:44 +0200 |
Cheers,Any idea why this might be the case?Thanks OleIt turned out to be some weird access issue, I think. When getting the error message I was running bammds on watt, whereas it worked fine on eos.
Morten--On Sun, Sep 7, 2014 at 12:54 PM, Ole Tange <address@hidden> wrote:On Sun, Sep 7, 2014 at 1:56 AM, Morten Allentoft
<address@hidden> wrote:
> Hi guys
>
> I'm getting an annoying error message that you perhaps can help me with?
>
> When I go:
> bammds MA840_L1_S2_trim15_PMDS_filter3.bam
> /k/genotypes/HGDP_hg19_one_allele.txt
>
> I get this:
> Error unlinking file tmp/EFD6SGwO2i using unlink0 at
> /usr/local/bin/bammds_parallel line 5150.
This should never happen.
It has most likely nothing to do with your data, but may have
something to do with your Linux environment.
I ran:
cd /tmp
bammds /home/meallentoft/data/Skhul/mapped_15bp/MA840_L1_S2_trim15_PMDS_filter3.bam
/k/genotypes/HGDP_hg19_one_allele.txt
and that works.
So that leads me to believe that the filesystem on
/home/meallentoft/data/Skhul/mapped_15bp is teasing you. If I look
right now, I see no 'tmp' dir there - and that is definitely bad, as
bammds creates that and uses that intensively. When finished
/home/meallentoft/data/Skhul/mapped_15bp/tmp should contain the same
as: /scratch/tange/tmp
Can you do this by hand:
cd /home/meallentoft/data/Skhul/mapped_15bp
mkdir tmp
and run it again? Do you get the same error?
/Ole
Morten E. AllentoftPostdoc, PhDCentre for GeoGeneticshttp://geogenetics.ku.dk+45 29 82 46 34 (mobile)Natural History MuseumØster Voldgade 5-7
DK-1350 Copenhagen
+45 35 32 12 91 (office)
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