LASTAL aborted

[walkyshitake]

Hello,

I am installing jcvi for synteny inference and visualization with MCscan. However, I keep encountering errors on LASTAL. I wonder if you could please take a look and provide any suggestions. My commands are listed below:

Installation for jcvi:

$ python3 -m venv jcvi_env
$ source jcvi_env/bin/activate
$ pip install jcvi
$ jcvi --version
jcvi 1.6.5

LASTAL:

$ wget https://gitlab.com/mcfrith/last/-/archive/1651/last-1651.tar.gz
$ tar -xzf last-1651.tar.gz
$ make

I put LASTAL within jcvi_env as:

$ ls jcvi_env
bin  include  last-1651  last-1651.tar.gz  lib  lib64  pyvenv.cfg  share

My running command is:

$ ls *.???
$ export PATH=./jcvi/jcvi_env/last-1651/bin:$PATH
$ python -m jcvi.compara.catalog ortholog BO BD --no_strip_names
[04/20/26 17:06:28] DEBUG    lastdb BD BD.cds                                                              base.py:1159

[04/20/26 17:12:57] DEBUG    lastal -u 0 -i3G -f BlastTab -P 4 BD BO.cds >./BO.BD.last                     base.py:1159

[04/20/26 17:25:34] ERROR    lastal failed with message:                                                   align.py:737
                             /bin/bash: line 1: 739133 Killed                  lastal -u 0 -i3G -f
                             BlastTab -P 4 BD BO.cds > ./BO.BD.last

[04/20/26 17:25:35] DEBUG    Failed to run `lastal` with multi-threading. Trying again.                    align.py:739
                    DEBUG    lastal -u 0 -i3G -f BlastTab -P 1 BD BO.cds >./BO.BD.last                     base.py:1159


[04/20/26 18:12:19] ERROR    lastal failed with message:                                                   align.py:749
                             /bin/bash: line 1: 739151 Killed                  lastal -u 0 -i3G -f
                             BlastTab -P 1 BD BO.cds > ./BO.BD.last

                    CRITICAL Failed to run `lastal`. Aborted.

I wonder if it is because of the path issue of LASTAL, or is it because of the memory limitation?

Many thanks
D

[Adamtaranto]

Try installing jcvi and LAST with conda.

https://anaconda.org/channels/bioconda/packages/jcvi/overview

[walkyshitake]

Hello,

I would like to follow up on that jcvi.compara.catalog ortholog often runs out of memory during analysis. I came across a similar discussion here (#809), but cannot locate synteny.py in my installation (conda). Could this indicate an incomplete installation, or might there be a different issue with my environment or package structure?

Also, would it be possible to run jcvi analyses on a digital cluster? If so, could you recommend appropriate memory and CPU allocations for typical genome comparisons?

Many thanks,
D