run "killed" at start - reasons?

[Sara Rocha]

Hi!

trying to run a big SNP dataset. It gets read OK but then quickly (1-2 minutes) process is killed...

can anyone give me any idea why or how to get more info? I tried --verbose but nothing else pops out... 

Bits of screenlog below:

Reading alignment file hake499.min4.fasta ... Fasta format detected

Name shortening took 0.000128 seconds.

Duplicate sequence name check took 0.000183 seconds.

Alignment most likely contains DNA/RNA sequences

Alignment has 449 sequences with 407966 columns, 407963 distinct patterns

87722 parsimony-informative, 30609 singleton sites, 289635 constant sites

[...]

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 98.525 seconds

Empirical state frequencies: 0.2301728983 0.3691522830 0.2830125140 0.1176623047 

Perform fast likelihood tree search using GTR+I+G model...

Estimate model parameters (epsilon = 5.0000000000)

Killed

any help appreciatted. Thanks!

[Heiko Schmidt]

Dear Sara,

Thank you for your interest in IQ-TREE.


From the output you have shown and my knowledge about
Linux/Unix systems, I guess that your IQ-TREE process
tried to allocate more memory than what the server has
to offer.

This is a reasonable guess, taking into account that
you have 407963 distinct patterns, i.e. unique columns
in your alignment.

An example of this can be found in
https://www.baeldung.com/linux/what-killed-a-process
in its section 3.3. There that have a process that grow
and grows the data structure “li” in Python until it gets
too large. At that point the System has to kill it to
prevent the server crashing by running out of memory.

You should check with your local system administrators
to figure out what exactly happens.
Your system admins should have access to dmesg (rf to
the above link) and the knowledge to interpret the
system message linked to your killed process.
Maybe they can give you access to a server that has enough
memory for your job.

To the best of my knowledge this is not a bug of
IQ-TREE, but a problem of the memory size of the server
used - however, without access to your server, one cannot
say more about it. Hence, please contact your sysadmins.

Best wishes,
Heiko

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Heiko Schmidt
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna / Max Perutz Labs
http://www.cibiv.at/
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