[Cytometry] Problems with backup data on network disk

Pouwels, W. w.pouwels at vumc.nl
Tue Nov 15 03:00:44 EST 2011


Hi Paolo,

The problem is due to the fact that Apple OS safes the actually file and it's type info separately (data fork /resource fork http://en.wikipedia.org/wiki/Resource_fork ). When copying to a windows server the resource fork get's 'lost' . 
This problem has been addressed before on this mailing list:

https://lists.purdue.edu/pipermail/cytometry/2010-October/039979.html

FacsConv should alleviate the 'problem' but is quite bothersome to use on large data sets. FlowJo e.g. doesn't mind the lost resource fork and will read the data anyway.

Greetings,

Walter

-----Original Message-----
From: cytometry-bounces at lists.purdue.edu [mailto:cytometry-bounces at lists.purdue.edu] On Behalf Of Josef Spidlen
Sent: Monday, November 14, 2011 7:31 PM
To: cytometry at lists.purdue.edu
Subject: Re: [Cytometry] Problems with backup data on network disk

Hi Paolo,
I am not sure what you mean by "PC" files; there is the $BYTEORD keyword 
in FCS that specifies the byte order (which is different on Mac/PC) but 
(i) I cannot see any backup software changing this, (ii) virtually all 
software tools can read "all" FCS byte orders. I guess you are simply 
copying your files to a network drive and then back to your system?

You may be having problems with the way your network drives are mounted. 
For example, if your network drive is a Windows-based share and your 
client runs on a Mac then you are using SMB (a native sharing protocol 
for Windows OS) and typically, you will lose file attributes (e.g., 
timestamps, user name, group name, read, write, and execute permissions 
for owner, group, and other) when transferring files there. This is due 
to limitations ofSMB and different implementation of file attributes on 
different systems. It could be that CellQuest is just setting some flags 
on these files and refuses reading them back if the flags have been 
changed? In this case, simply using a different file system on the 
server may not help.

Have you tried packing the files into some kind of container format that 
keeps all the file attributes (e.g., tar.gz). If you pack the files to a 
tar.gz file, than copy to your network, than retrieve from your network 
and extract from the tar.gz, then you should (hopefully) be able to read 
these back in CellQuest.

Cheers,
Josef


On 11-11-10 05:57 AM, NMS, Svc_facs [Service] wrote:
>
> Dear All,
>
> We have to backup data (CellQuest data and fcs files)coming from
> CellQuest acquisition to network disk (I assume should be Windows
> formatted). When I backup files and I restore from network disk to local
> disk, data appears as "pc" files unreadable by CQ and only way to
> recovery data is using older FACSConvert program (usable for small data
> sets).
> Is there a way to overcome this problem such as using a different type
> of disk formatting?
> Many regards to all help us to fix this problem.
> PC
>
> ________________________________________
>
> Paolo Cappella, Dr. Biol.
> Cell Assays Technologies / Flow Cytometry
> Building 75 - Discovery
> Nerviano Medical Sciences srl
> PO Box 11 - Via Pasteur 10
> 20014 Nerviano MI
> phone: office +390331581367
>             lab    +390331581778
>             cell   +393389003111
> website www.nervianoms.com
>
>
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-- 
Josef Spidlen, Ph.D.
Terry Fox Laboratory, BC Cancer Agency
675 West 10th Avenue, V5Z 1L3 Vancouver, BC, Canada

Tel: +1 (604) 675-8000 x 7755
http://www.terryfoxlab.ca/people/rbrinkman/josef.aspx


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