Howdy, Andrew,
One possibility is that there are more jobs on the cluster. I'm not
familiar enough with the galaxy interface to know if there's an easy
way to tell how much time the job sits on the cluster's queue waiting
and how much time the job is actually running.
Assuming there's no
Hi - is there a reason Lastz is very slow right now? I am mapping 2-3,000,
reads against a single, 11Kb, sequence and find that jobs are either returning
an error or taking 16-24hrs to get done. This time frame was more like 30
minutes two weeks ago. Is there a way to speed this up? Thanks in ad
On Nov 12, 2011, at 6:30 AM, Andrew South wrote:
> Dear Nate -
>
> It seems I may have upset the cluster again: I have 3 Lastz jobs running and
> cannot upload any more data. I had been uploading fine; started 3 lastz
> mapping jobs (Fasta (1 sequence) vs Fasta (~3000 sequences) output as SNP
Dear Nate -
It seems I may have upset the cluster again: I have 3 Lastz jobs running and
cannot upload any more data. I had been uploading fine; started 3 lastz mapping
jobs (Fasta (1 sequence) vs Fasta (~3000 sequences) output as SNP, when I
realised I made a mistake, cancelled these jobs,
On Nov 11, 2011, at 10:01 AM, Andrew South wrote:
> Thanks Nate, hope it's a quick fix. Best wishes, Andy
Hi Andy,
All backlogged NGS jobs should now be running, new ones will likely queue until
free slots are available. Please let us know if there's further trouble, and
thanks for using Gala
On Nov 11, 2011, at 9:21 AM, Andrew South wrote:
> Hello folks
>
> Anyone else having trouble with running Lastz to map?
>
> Jobs are being sent but not running.
>
> It stopped working for me two days ago after working perfectly, I've tried
> fiddling with the formats but no joy.
Hi And
Hello folks
Anyone else having trouble with running Lastz to map?
Jobs are being sent but not running.
It stopped working for me two days ago after working perfectly, I've tried
fiddling with the formats but no joy.
Thanks,
Andy
Dr A P South
Centre for Oncology and Molecular Med
Gesendet: Montag, 6. Juni 2011 18:06
An: Appelt, Uwe
Cc: galaxy-user@lists.bx.psu.edu
Betreff: Re: [galaxy-user] LASTZ arguments in "Full parameter list"-mode
Howdy, Uwe,
(I don't speak for the galaxy group, but I watch the list for lastz-
related messages.)
> Is it pos
Howdy, Uwe,
(I don't speak for the galaxy group, but I watch the list for lastz-
related messages.)
Is it possible to specify more arguments in "Full parameter list"-
mode, particularly those that're implicitely described in YASRA-mode
(match/mismatch rewards and step-size (Z/step))?
As y
Hi @All,
short version:
Is it possible to specify more arguments in "Full parameter list"-mode,
particularly those that're implicitely described in YASRA-mode (match/mismatch
rewards and step-size (Z/step))?
long version:
I'm dealing with 454 reads and it's crucial to the scenario to have the 5
..
Alex
Van: galaxy-user-boun...@lists.bx.psu.edu
[galaxy-user-boun...@lists.bx.psu.edu] namens Bob Harris [rshar...@bx.psu.edu]
Verzonden: maandag 21 maart 2011 22:04
Aan: JASON G. BANKERT
CC: galaxy-u...@bx.psu.edu
Onderwerp: Re: [galaxy-user] LASTZ: Controlling L
On Mar 21, 2011, at 1:45 PM, JASON G. BANKERT wrote:
We're trying to only get hits of certain lengths. Is there a
setting to use that sets the minimum length for each hit?
The short answer is no, but I expect there are other tools in galaxy
that could do that filtering.
There are two reas
On Mar 21, 2011, at 1:45 PM, JASON G. BANKERT wrote:
We're trying to only get hits of certain lengths. Is there a
setting to use that sets the minimum length for each hit?
Howdy, Jason,
Lastz (the underlying program) has some options that are geared toward
filtering by length, though none
We're trying to only get hits of certain lengths. Is there a setting to use
that sets the minimum length for each hit?
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