aBSREL run error

[luisasegovia]

Hi there! I keep getting this error pop up when I run aBSREL with my data set. This is the error message I have been getting every time I run aBSREL. I only have this issue with this data set so I am not sure what I can do to avoid this message. I am using a partition data set I got from GARD. Thank you.

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

[n7:41321] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n7:41321] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n7:41321] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n7:41321] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n7:41321] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n7:41321] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n7:41321] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 HYPHYMPI terminated. Error: HyPhy killed by signal 15

[stevenweaver]

Dear @luisasegovia,

Does this error occur when using hyphy on Datamonkey or on your server?

Best, Steven

[luisasegovia]

Hi. It occurs when I use hyphy on datamonkey.

[spond]

Dear @luisasegovia,

Could you share your Datamonkey URL here?

Best, Sergei

[luisasegovia]

Yup. Here's the link: http://datamonkey.org/absrel/63472b6835d8215fcb2fd88c

[spond]

Dear @luisasegovia,

Thank you. Let me take a quick look...

Best, Sergei

[luisasegovia]

Thank you for your help!

[spond]

Dear @luisasegovia,

Doh, I am not thinking clearly today. Looking at the logs, I see

Master node received an error:aBSREL only works on a single partition dataset in call to assert(utility.Array1D(absrel.partitions_and_trees)==1, error_msg);

Function call stack
1 :  assert(utility.Array1D(absrel.partitions_and_trees)==1, error_msg);
-------
2 :  ExecuteCommands("assert (`statement`, error_msg)", /home/datamonkey/datamonkey-js-server/production/app/absrel/../../.hyphy/res/TemplateBatchFiles/libv3/);
-------
3 :  io.CheckAssertion("utility.Array1D (absrel.partitions_and_trees) == 1","aBSREL only works on a single partition dataset");
-------

aBSREL does not support multiple partition datasets (because the set of branches has to be the same for all sites). Datamonkey does not report this particular error to you, which is our oversight and is confusing. You can see the error if you click on

I would suggest partitioning your data into individual non-recombinant fragments and then running aBSREL

Many other analyses (BUSTED, FEL, MEME) do support multiple partitions, though.

Best, Sergei

[stevenweaver]

The logging issue has been an open issue for quite some time. Linking veg/datamonkey-js#197 to increase awareness.

[luisasegovia]

Whoops sorry! I'll close it right away

[akarimizade]

Hi! I also have the issue with the same error. https://www.datamonkey.org/absrel/63ca6712c82f520f6a311bc3 MEME test worked properly, but when I use aBSREL, it gives me an error.