Re: [Bammds-users] ASD file error

[Morten Allentoft]

Thanks Ole and Victor!

Bammds now runs fine when logged into watt.

Cheers,

Morten

On Sun, Sep 7, 2014 at 5:17 PM, Ole Tange <address@hidden> wrote:

I think I nailed it.

I have overwritten /home/sapfo/install/bin/bammds_parallel with GNU
Parallel version 20140907, which is the program used by bammds.

Please see if that that works.

/Ole

On Sun, Sep 7, 2014 at 4:52 PM, Ole Tange <address@hidden> wrote:
> Victor's suggestion is along the same lines as mine: Try to put the
> 'tmp' dir on a local file system and not on a NFS-mounted filesystem.
>
> I have just been able to reproduce your error:
>
>   cd ~/data
>   seq 1 | TMPDIR=. bammds_parallel echo
>   Error unlinking file ./eKEo4j8p2o using unlink0 at
> /usr/local/bin/bammds_parallel line 5150.
>
> And it is clearly not an error that exists in GNU Parallel < 20131222,
> so it is likely fixable.
>
> Until I get that fixed, do not use a NFS-mounted dir as the tmpdir.
>
> /Ole
>
> On Sun, Sep 7, 2014 at 4:16 PM, José Víctor Moreno Mayar
> <address@hidden> wrote:
>> Hey Morten,
>>
>> Can you try running this on watt before running bammds?
>>
>> export TMPDIR=$HOME/scratch
>>
>> Víctor
>>
>> On Sun, Sep 7, 2014 at 4:07 PM, Morten Allentoft
>> <address@hidden> wrote:
>>>
>>> Thanks Ole
>>>
>>> It 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.
>>>
>>> Any idea why this might be the case?
>>>
>>> Cheers,
>>> 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. Allentoft
>>> Postdoc, PhD
>>>
>>> Centre for GeoGenetics
>>> Natural History Museum
>>> Øster Voldgade 5-7
>>> DK-1350 Copenhagen
>>>
>>> +45 35 32 12 91 (office)
>>> +45 29 82 46 34 (mobile)
>>> http://geogenetics.ku.dk
>>>
>>> Sign up for our newsletter!
>>
>>
>>
>>
>> --
>> José Víctor Moreno Mayar
>> Centre for GeoGenetics
>> University of Copenhagen

--

Morten E. Allentoft

Postdoc, PhD

Centre for GeoGenetics

Natural History Museum

Øster Voldgade 5-7
DK-1350 Copenhagen

+45 35 32 12 91 (office)

+45 29 82 46 34 (mobile)

http://geogenetics.ku.dk

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