[Cytometry] Problems with backup data on network disk
w.pouwels at vumc.nl
Tue Nov 15 03:00:44 EST 2011
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:
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.
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
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.
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
> 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.
> 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
> This message has been scanned for malware by Websense. www.websense.com
> Cytometry mailing list
> Cytometry at lists.purdue.edu
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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
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