Error: parsing file part.txt failed; character has changed from '\3' to '/3'
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Debajyoti Kabiraj
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'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'.
Alexandros Stamatakis
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
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Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
www.exelixis-lab.org
"the notation for choosing every n-th (e.g., triplet)
character has changed from '\3' to '/3'"
Aexis
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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
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,
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
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
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
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
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:
>>
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
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.
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
Debajyoti
Alexandros Stamatakis
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:>
> <https://groups.google.com/d/msgid/exabayes/7a4864b9-4ed1-40b3-b82f-777c85506633o%40googlegroups.com?utm_medium=email&utm_source=footer>.
Please have a look at the detailed manual:
https://cme.h-its.org/exelixis/web/software/exabayes/index.html
Alexis
> > 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
>
> > 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
>
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