Raxml-PTHREADS-SSE3 (Fast bootstrap) terminates mid-way without any error message

[Nachiket Shankar]

I'm running a raxml - fast bootstrap for a multiple alignment of short sequences. 

Command : nohup `for i in *.phy; do raxmlHPC-PTHREADS-SSE3 -s $i -n $i.out  -m GTRGAMMAI -T 8 -f a -x 13 -N 500 > $i.log; done` &

The process terminates randomly while bootstrapping. I've attached the ".log" file and the ".out" file

Please help me if possible. 

Thanks,

Nachiket

[Alexandros Stamatakis]

can you please upgrade to RAxMl version 8.0.6

https://github.com/stamatak/standard-RAxML/releases

and then let me know if the error is still there.

Also, judging by your script below it seems that you may be
over-subscribing the cores on the node you are using, each thread should
run on a separate physical core.

Alexis

On 02/25/2014 11:27 AM, Nachiket Shankar wrote:
> I'm running a raxml - fast bootstrap for a multiple alignment of short
> sequences.
>

> Command : *nohup `for i in *.phy; do raxmlHPC-PTHREADS-SSE3 -s $i -n $i.out
> -m GTRGAMMAI -T 8 -f a -x 13 -N 500 > $i.log; done` &*

>
> The process terminates randomly while bootstrapping. I've attached the
> ".log" file and the ".out" file
>
> Please help me if possible.
>
> Thanks,
>
> Nachiket
>

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Nachiket Shankar]

I installed the latest version of raxml from here : 

https://github.com/stamatak/standard-RAxML

However, now I am getting

Error message: 

----xxxx----

raxmlHPC-PTHREADS-SSE3: fastDNAparsimony.c:137: checkSeed: Assertion `adef->parsimonySeed > 0' failed.

nohup: missing operand

Try `nohup --help' for more information.

^C

[1]+  Exit 125                nohup `for i in *.phy; do raxmlHPC-PTHREADS-SSE3 -s $i -n $i.out  -m GTRGAMMAI -T 8 -f a -x 13 -N 500 > $i.log; done`

----xxxx----

Nachiket

--
You received this message because you are subscribed to a topic in the Google Groups "raxml" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/raxml/dBu31ZVYgWE/unsubscribe.
To unsubscribe from this group and all its topics, send an email to raxml+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.

[Alexandros Stamatakis]

you need to specify a random number seed via -p, please see previous
posts on this group about this,

alexis

>> raxml+un...@googlegroups.com.

>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>