[BioC] Using easyRNASeq package: question about BAM/BAI and links to them

Martin Morgan mtmorgan at fhcrc.org
Tue Nov 26 19:10:24 CET 2013

On 11/26/2013 09:36 AM, Sylvain Foisy Ph. D. wrote:
> Hi,
> On 2013-11-26, at 11:55 AM, Nicolas Delhomme wrote:
>> 1) Is there any possibility that you have circular symlinks, or symlink chains? I’m not sure how gracefully R would do with symlink chains.
> Nope, I checked for that.
>> 2) Are there no permission issues on the bam/bai files or a subset of them?
> Nope take 2: both locations are own by me with full r+w permissions
>> 3) Could it be that the symlink names are too long? That used to create problem in the distant past on some linux distro, but I have not seen it occurring in years.
> I made it work when I am in the original location (a single BAM/BAI combo) and it works so the hypothesis of long paths might be it...  I'll see what I can do to rename my stuff with shorter names.

my guess would be cross-file-system symlinks. Martin

> Thanks for the time
> Sylvain
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