Groups
Sign in
Groups
CIPRES Science Gateway Users
Conversations
About
Send feedback
Help
CIPRES Science Gateway Users
Contact owners and managers
1–30 of 258
Welcome CIPRES users. This forum is for sharing questions and issues in using the CIPRES resource.
Mark all as read
Report group
0 selected
Dhananjay
,
Mark Miller
2
11:12 AM
Unable to access CIPRES science gateway
Hi there, Thanks for reporting the issue. It looks like you registered in both places. But the portal
unread,
Unable to access CIPRES science gateway
Hi there, Thanks for reporting the issue. It looks like you registered in both places. But the portal
11:12 AM
Giuseppe Emanuele De Pasquale
,
Mark Miller
2
May 9
Slowness of MrBayes due to partitioning or missing Nexus block parameters?
Hi all, my colleague, Wayne Pfeiffer, manages efficiency here at CIPRES. He has this response: Hi
unread,
Slowness of MrBayes due to partitioning or missing Nexus block parameters?
Hi all, my colleague, Wayne Pfeiffer, manages efficiency here at CIPRES. He has this response: Hi
May 9
Dave Id
, …
Mark Miller
8
May 9
Generate MrBayes block from IQ-TREE
Great, thanks for doing that. As I understand it currently, we have to understand and specify the
unread,
Generate MrBayes block from IQ-TREE
Great, thanks for doing that. As I understand it currently, we have to understand and specify the
May 9
Allan Sampao
,
Mark Miller
2
May 6
Activation email
Hi Allan, Sometimes the activation message gets blocked by your local administrative policies. It
unread,
Activation email
Hi Allan, Sometimes the activation message gets blocked by your local administrative policies. It
May 6
Ziv Lieberman
,
Mark Miller
4
May 2
IQ-TREE: Merge partitions only?
The patch is in place now, so by default, bootstrapping is not selected. On Thursday, May 2, 2024 at
unread,
IQ-TREE: Merge partitions only?
The patch is in place now, so by default, bootstrapping is not selected. On Thursday, May 2, 2024 at
May 2
yue meng
,
Mark Miller
2
Apr 18
There is no confirmation option in the registration confirmation email, how can I verify it?
Hi there, It looks like you didnt receive the activation email. Sometimes it gets caught in a spam
unread,
There is no confirmation option in the registration confirmation email, how can I verify it?
Hi there, It looks like you didnt receive the activation email. Sometimes it gets caught in a spam
Apr 18
D Redding
,
Mark Miller
2
Mar 15
Problem with CIPRES subscription
Hi Dave, Thanks for reporting the issue. Credit should appear instantly in the interface, so there
unread,
Problem with CIPRES subscription
Hi Dave, Thanks for reporting the issue. Credit should appear instantly in the interface, so there
Mar 15
Mario Sandoval
,
Mark Miller
5
Mar 13
Unable to upload files to CIPRES endpoint - Globus Transfer
Dear Mario, We investigated this issue on our side. We found that activating the endpoint is key.
unread,
Unable to upload files to CIPRES endpoint - Globus Transfer
Dear Mario, We investigated this issue on our side. We found that activating the endpoint is key.
Mar 13
Harilaos Lessios
,
Mark Miller
3
Feb 29
Problem with IMa3
Just a quick update: this issue is resolved, and the requested feature works. Mark On Tuesday,
unread,
Problem with IMa3
Just a quick update: this issue is resolved, and the requested feature works. Mark On Tuesday,
Feb 29
Ligia Benavides
,
Mark Miller
3
Feb 26
phylobayes on cipres
Hi there Ligia, It should work now, let me know if you have a further issue. Mark On Monday, February
unread,
phylobayes on cipres
Hi there Ligia, It should work now, let me know if you have a further issue. Mark On Monday, February
Feb 26
Rodolfo Probst
,
Mark Miller
4
Feb 23
Issues with IQ-Tree Run
Thanks for letting me know Rodolfo. I understand about the free tier and time issue; you found a good
unread,
Issues with IQ-Tree Run
Thanks for letting me know Rodolfo. I understand about the free tier and time issue; you found a good
Feb 23
prabodh bajpai
,
Mark Miller
2
Feb 19
Identifying correct output in MAFFT alignment
Hi Prabodh, Thanks for the inquiry. progress.mafft should give you information about the progress of
unread,
Identifying correct output in MAFFT alignment
Hi Prabodh, Thanks for the inquiry. progress.mafft should give you information about the progress of
Feb 19
周亚彬
,
Mark Miller
2
Feb 8
Data queued issue
Hi there, I sincerely apologize for this issue. In both cases a user (two different users) uploaded
unread,
Data queued issue
Hi there, I sincerely apologize for this issue. In both cases a user (two different users) uploaded
Feb 8
Mark Miller
Feb 5
upcoming maintenance: jobs will be held
Dear Users, On Monday 2/12, there will be a maintenance that kills running jobs. The maintenance will
unread,
upcoming maintenance: jobs will be held
Dear Users, On Monday 2/12, there will be a maintenance that kills running jobs. The maintenance will
Feb 5
Celeste Mouth
,
Mark Miller
2
Feb 1
Data queued for 3 days
Hi Celeste, Thanks for reporting the issue. Unfortunately one user uploaded 20000 files all at once
unread,
Data queued for 3 days
Hi Celeste, Thanks for reporting the issue. Unfortunately one user uploaded 20000 files all at once
Feb 1
Aimee Caye Chang
,
Mark Miller
4
Jan 29
Missing file on Mr. Bayes
Awesome, thanks for letting me know. Probably it eas a node failure or something like that that
unread,
Missing file on Mr. Bayes
Awesome, thanks for letting me know. Probably it eas a node failure or something like that that
Jan 29
Aimee Caye Chang
Jan 27
Mr. Bayes problem
Hi, I am having problems running Mr. Bayes today. Below was the first attempt that said the run was
unread,
Mr. Bayes problem
Hi, I am having problems running Mr. Bayes today. Below was the first attempt that said the run was
Jan 27
Mattia Ragazzini
,
Mark Miller
2
Jan 26
MrByes on XSEDE stops likely for input error
Hi Mattia, A couple of things: I found no CIPRES account associated with the email address you sent
unread,
MrByes on XSEDE stops likely for input error
Hi Mattia, A couple of things: I found no CIPRES account associated with the email address you sent
Jan 26
jhorn
,
Mark Miller
2
Jan 25
MrBayes on XSEDE repeatedly stoping after 331000 generations
Hi Jay, Your runs stopped because they reached the configured stoprun value: In the parameters, it
unread,
MrBayes on XSEDE repeatedly stoping after 331000 generations
Hi Jay, Your runs stopped because they reached the configured stoprun value: In the parameters, it
Jan 25
prs...@gmail.com
, …
Mark Miller
25
Jan 24
Q&A
Error runing ParallelStructure
Hi Rodrigo, Thanks very much for letting me know. The parallelstructure code has pretty weak error
unread,
Q&A
Error runing ParallelStructure
Hi Rodrigo, Thanks very much for letting me know. The parallelstructure code has pretty weak error
Jan 24
Jeremy Miller
,
Mark Miller
3
Jan 23
BEAST2-TreeAnnotator EOF error
Hi Mark, Thanks for your thoughts on this issue. I tried a couple of runs to explore this, with
unread,
BEAST2-TreeAnnotator EOF error
Hi Mark, Thanks for your thoughts on this issue. I tried a couple of runs to explore this, with
Jan 23
Muhammad Azeem Khan
,
Mark Miller
2
Jan 3
Not working.
Sorry for the late reply, NCL converter is working fine. It may have been down from a temporary
unread,
Not working.
Sorry for the late reply, NCL converter is working fine. It may have been down from a temporary
Jan 3
Mark Miller
2
12/11/23
CIPRES will undergo maintenance 7 AM Pacific 12/11/2023 - 7 AM 12/12/2023
Dear Users, We just learned the scheduled maintenance has been pushed out to Monday 12/18/2023. Sorry
unread,
CIPRES will undergo maintenance 7 AM Pacific 12/11/2023 - 7 AM 12/12/2023
Dear Users, We just learned the scheduled maintenance has been pushed out to Monday 12/18/2023. Sorry
12/11/23
Darko Cotoras
,
Mark Miller
7
11/14/23
No output file in ModeltTest-NG, if -s=203
Thank you for forwarding the message to the MODELTEST-NG google group, Mark. I look forward to their
unread,
No output file in ModeltTest-NG, if -s=203
Thank you for forwarding the message to the MODELTEST-NG google group, Mark. I look forward to their
11/14/23
Mark Miller
11/8/23
Popeye is odwn temporarily, (MrBayes restarts will not work temporarily)
Hi all, The Popeye machine is currently down. MrBayes runs have been moved to Expanse, and will work
unread,
Popeye is odwn temporarily, (MrBayes restarts will not work temporarily)
Hi all, The Popeye machine is currently down. MrBayes runs have been moved to Expanse, and will work
11/8/23
Sone Janse van Rensburg
,
Mark Miller
2
10/14/23
Trouble processing BI info
Hi there, With MB, and many other codes, the first step is to look at the files stderr.txt and stdout
unread,
Trouble processing BI info
Hi there, With MB, and many other codes, the first step is to look at the files stderr.txt and stdout
10/14/23
Max Laubstein
,
Mark Miller
3
9/28/23
Resuming BEAST 2 run
Here is a link showing the basic process for restarting" http://www.phylo.org/tools/html5/
unread,
Resuming BEAST 2 run
Here is a link showing the basic process for restarting" http://www.phylo.org/tools/html5/
9/28/23
Mark Miller
8/15/23
Maintenance on the Expanse machine is completed
New jobs can be submitted now.
unread,
Maintenance on the Expanse machine is completed
New jobs can be submitted now.
8/15/23
RITUPARNA SAHA
,
Miller, Mark
2
7/3/23
application for checking submission has been terminated every time
Hi there, Sorry for the inconvenience, this should be working again. Let me know if you have any
unread,
application for checking submission has been terminated every time
Hi there, Sorry for the inconvenience, this should be working again. Let me know if you have any
7/3/23
Mark Miller
5/26/23
Command not found for RAXML, RAXMLNG, READSEQ, and REVBAYES runs
If you received a message like this in the past 12-16 hours: /expanse/projects/ngbt/backend/
unread,
Command not found for RAXML, RAXMLNG, READSEQ, and REVBAYES runs
If you received a message like this in the past 12-16 hours: /expanse/projects/ngbt/backend/
5/26/23