Error: parsing file part.txt failed; character has changed from '\3' to '/3'

56 views
Skip to first unread message

Debajyoti Kabiraj

unread,
May 27, 2020, 3:05:42 AM5/27/20
to ExaBayes
Dear Expert,

I'm running Exabayes for the first time in CIPRES Gateway using Phylip file of concatenated 335 genes (DNA Sequences)  also used partition file a configuration file. However, It shows an Error during the parsing partition file...

I have checked my partition file but could not get any ambiguity. I have attached all files along with this post.
It will be an immense help for me if someone kindly corrects me.

Thanks,

Debajyoti

Error: parsing file part.txt failed. 

Please double-check, whether each site is assigned a partition. 
Side note: the notation for choosing every n-th (e.g., triplet) 
character has changed from '\3' to '/3'.
335_Config_1.nex
335_Part.part

Alexandros Stamatakis

unread,
May 27, 2020, 5:59:23 AM5/27/20
to exab...@googlegroups.com
Did you take intoi account this note in the error message?

"the notation for choosing every n-th (e.g., triplet)
character has changed from '\3' to '/3'"

in your partition file you use: \3 instead of /3

Aexis
> --
> You received this message because you are subscribed to the Google
> Groups "ExaBayes" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to exabayes+u...@googlegroups.com
> <mailto:exabayes+u...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/exabayes/5de5fe9a-dd5c-493d-bacc-c76b6d35eb3f%40googlegroups.com
> <https://groups.google.com/d/msgid/exabayes/5de5fe9a-dd5c-493d-bacc-c76b6d35eb3f%40googlegroups.com?utm_medium=email&utm_source=footer>.

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

Debajyoti Kabiraj

unread,
Jun 2, 2020, 9:44:57 PM6/2/20
to ExaBayes
Respected Sir,

Thank you very much for your kind response. However, I have tried with /3 but got another error,

Command used
exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3

Error :

exabayes: ./src/mcmc/CoupledChains.cpp:383: void CoupledChains::executePart(uint64_t, uint64_t, ParallelSetup&): Assertion `_chains[remoteId].getGeneration() == swap.getGen()' failed.
[comet-29-57:11365] *** Process received signal ***
[comet-29-57:11365] Signal: Aborted (6)
[comet-29-57:11365] Signal code:  (-6)
[comet-29-57:11365] [ 0] /usr/lib64/libpthread.so.0(+0xf5d0)[0x2addd8c725d0]
[comet-29-57:11365] [ 1] /usr/lib64/libc.so.6(gsignal+0x37)[0x2addd8eb5207]
[comet-29-57:11365] [ 2] /usr/lib64/libc.so.6(abort+0x148)[0x2addd8eb68f8]
[comet-29-57:11365] [ 3] /usr/lib64/libc.so.6(+0x2f026)[0x2addd8eae026]
[comet-29-57:11365] [ 4] /usr/lib64/libc.so.6(+0x2f0d2)[0x2addd8eae0d2]
[comet-29-57:11365] [ 5] exabayes[0x442a39]
[comet-29-57:11365] [ 6] exabayes[0x42ba5b]
[comet-29-57:11365] [ 7] exabayes[0x40b48a]
[comet-29-57:11365] [ 8] exabayes[0x40d2e5]
[comet-29-57:11365] [ 9] exabayes[0x40846c]
[comet-29-57:11365] [10] /usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2addd8ea13d5]
[comet-29-57:11365] [11] exabayes[0x409eaf]
[comet-29-57:11365] *** End of error message ***
/projects/ps-ngbt/home/cipres/ngbw/contrib/tools/bin/exabayes_wrapper_1.5_centos7: line 10: 11365 Aborted                 (core dumped) exabayes $*
srun: error: comet-29-57: task 53: Exited with exit code 134
srun: First task exited 30s ago
srun: tasks 0-52,54-71: running
srun: task 53: exited abnormally
srun: Terminating job step 33840233.0
srun: Job step aborted: Waiting up to 302 seconds for job step to finish.
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9902 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9915 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9911 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9908 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9900 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9919 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9921 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9899 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9910 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9901 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9904 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9903 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9913 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9914 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9917 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9920 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9909 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9905 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  9918 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
slurmstepd: *** STEP 33840233.0 ON comet-07-50 CANCELLED AT 2020-06-02T08:29:09 ***
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29332 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29326 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29329 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29333 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29343 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29325 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2781 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2761 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2771 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2780 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2773 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2778 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29338 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29330 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29327 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2766 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2769 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2783 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2772 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2775 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2777 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2776 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29328 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29324 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29331 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29346 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29334 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2770 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2768 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2774 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29337 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2782 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2764 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29342 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2763 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29341 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3:  2762 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29345 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29339 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29340 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-EXABAYES_XSEDE-D0BCEC6E49574D8F9A4FB1338B2386FD/./_batch_command.cmdline: line 3: 29335 Killed                  exabayes_wrapper_1.5_centos7 -m DNA -f infile.phy -R 2 -C 2 -s 12345 -q part.txt -n 335_Exa_part -c config.nex -M 3
srun: error: comet-29-57: tasks 48-52,54-66,71: Exited with exit code 137
srun: error: comet-29-57: tasks 67-70: Killed
srun: error: comet-07-50: tasks 0-16,18-20,22: Exited with exit code 137
srun: error: comet-07-50: tasks 17,21,23: Killed
srun: error: comet-17-17: tasks 24-39,41-42,44,46: Exited with exit code 137
srun: error: comet-17-17: tasks 40,43,45,47: Killed
 
Regards,

Debajyoti

Andre Aberer

unread,
Jun 5, 2020, 1:14:27 AM6/5/20
to exab...@googlegroups.com
Hello Debajyoti,

I think, the error you are seeing is unrelated to your partition file.

With your given swapping runtime configuration, a bug occurs. My
suggestion is to remove the '-C 2' from your command line.

--
Best regards,
Andre

Debajyoti Kabiraj

unread,
Jun 13, 2020, 11:31:39 AM6/13/20
to ExaBayes
Dear Sir,

Thanks for your suggestion, after that I was running the CONSENSE program in CIPRES using topology file Exabayes analysis it shows below error,
Kindly suggest how to correct it

Settings for this run:
 C         Consensus type (MRe, strict, MR, Ml):  Majority rule (extended)
 R                Trees to be treated as Rooted:  Yes
 T           Terminal type (IBM PC, ANSI, none):  (none)
 1                Print out the sets of species:  Yes
 2         Print indications of progress of run:  Yes
 3                               Print out tree:  Yes
 4               Write out trees onto tree file:  Yes

Are these settings correct? (type Y or the letter for one to change)
ERROR:  This program has caused a Segmentation fault.
       This may have been caused by an incorrectly formatted input file
       or input tree file.  You should check those files carefully.
       If this seems to be a bug, please mail j...@gs.washington.edu
       with the name of the program, your computer system type,
       a full description of the problem, and with the input data file.
       (which should be in the body of the message, not as an Attachment).

Regards,

Debajyoti Kabiraj

Andre Aberer

unread,
Jun 14, 2020, 5:48:15 AM6/14/20
to exab...@googlegroups.com
Hi Debajyoti,

the output you are showing does not belong the 'consense' program that
belongs to ExaBayes, but to Joe Felsenstein's software suite.

Please talk to your local administrator how the 'consense' binary by
ExaBayes can be accessed (potentially it has been renamed to
'consense-exabayes') or you just need to figure out the full path to the
program.

--
Best regards,
Andre

Debajyoti Kabiraj writes:

>>

Debajyoti Kabiraj

unread,
Jul 8, 2020, 1:06:27 AM7/8/20
to ExaBayes
Dear Sir,

Thank you for the support, now these things are working well after getting suggestions from with Prof. Felsenstein.

However, kindly let me know how can I add posterior probability and branch length value at the tree.

Thanks,
Debajyoti

Alexandros Stamatakis

unread,
Jul 8, 2020, 2:14:38 AM7/8/20
to exab...@googlegroups.com
Dear Debajyoti,

Please have a look at the detailed manual:

https://cme.h-its.org/exelixis/web/software/exabayes/index.html

Alexis
> j...@gs.washington.edu <javascript:>
> >        with the name of the program, your computer system type,
> >        a full description of the problem, and with the input data
> file.
> >        (which should be in the body of the message, not as an
> Attachment).
> >
> >
> > Regards,
> >
> > Debajyoti Kabiraj
>
> --
> You received this message because you are subscribed to the Google
> Groups "ExaBayes" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to exabayes+u...@googlegroups.com
> <mailto:exabayes+u...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/exabayes/7a4864b9-4ed1-40b3-b82f-777c85506633o%40googlegroups.com
> <https://groups.google.com/d/msgid/exabayes/7a4864b9-4ed1-40b3-b82f-777c85506633o%40googlegroups.com?utm_medium=email&utm_source=footer>.
Reply all
Reply to author
Forward
Message has been deleted
0 new messages