LiftOver chain file generation for nothobranchius furzeri

[B. Osberg]

Dear UCSC staff:

I'm a postdoc at the Max Planck Institute for Molecular Genetics, and
I'm trying to map some genomic coordinates from the human genome to that
of another species, nothobranchius furzeri
(https://www.nothobranchius.info/). My first thought was to use your
program LiftOver (thank you for making it available!), however the
furzeri genome is not included in the reference genomes listed on the
web API (http://genome.ucsc.edu/cgi-bin/hgLiftOver). Hence, I'm
attempting to build the necessary chain files from scratch, following
the directions provided here :
http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl

It seems that some of the software at that latter link is specific to
the architecture on your system, however. For example, the [Parasol Job
Control System](
http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl#Parasol_Job_Control_System
) is timing out when I run it on our servers here in Berlin:

para make jobList
rudpSend timed out
pmSendString timed out!
pmSendString: will sleep 60 seconds and retry
rudpSend timed out
pmSendString timed out!
pmSendString: will sleep 60 seconds and retry
...

Have you encountered this problem before, and do you know if there is a
way to generalize this software so I can run it on a local interactive
node ? perhaps there might be an update or some other documentation for
chain-file generation besides the link above? If generating the full
chain full is not possible, then I'll look into alignment of individual
locus sequences, but I thought this was worth a try.

Thanks very much again for providing this resource for the community,
and for any advise you may have for how to best make use of it.

best regards,

Brendan Osberg

[Hiram Clawson]

Good Morning Brenden:

I'm curious if this installation procedure and example test
worked for you:

http://genomewiki.ucsc.edu/index.php/Parasol_job_control_system

Is this the genome assembly you are working with:

https://genome.ucsc.edu/h/GCF_001465895.1

--Hiram