Minimap2 will not run

[peradastra]

Hello RA team,

Installed RA following instructions without error.
However when i try to run the following command...
python ../../scripts/ra/build/bin/ra -t 16 -x pb pacbio.fasta
I get the following error...
[Ra::run] preconstruction overlap stage
[Ra::run] error: unable to run minimap2!
[Ra::exit] warning: unable to clean work directory!

Any advice?
I've tried changing how Minimap2 is called but it's still not working.

Brian

[rvaser]

Hello Brian,
can you please run head -n 20 ../../scripts/ra/build/bin/ra and paste the output here?

Best regards,
Robert

[peradastra]

Hey Robert, I actually just re-cloned and reinstalled ra. It now appears to be running fine. Will email again if I run into an interesting issue. Sorry! Brian

…

On Nov 29, 2018, at 4:24 AM, Robert Vaser ***@***.***> wrote: Hello Brian, can you please run head -n 20 ../../scripts/ra/build/bin/ra and paste the output here? Best regards, Robert — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALWv8VYQnE1Gscnvym79Qxf_n4YHvbijks5uz7XNgaJpZM4Y4n40>.

[peradastra]

Hey Robert, So the pipeline ran and produced and assembly graph (rala_assembly_graph.gfa) but no fasta. I ran this on a separate screen on our cluster and when I pull up that screen there’s a bunch of sequence that was printed out. So I’m not sure if it is not generating a fasta file and instead printing out the sequence or what. Any advice? Brian P.S. My command was python /home/brian/scripts/ra/build/bin/ra -t 32 -x pb pacbio_all.fasta

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On Nov 29, 2018, at 8:06 AM, Brian-Tyler St.Hilaire ***@***.***> wrote: Hey Robert, I actually just re-cloned and reinstalled ra. It now appears to be running fine. Will email again if I run into an interesting issue. Sorry! Brian > On Nov 29, 2018, at 4:24 AM, Robert Vaser ***@***.*** ***@***.***>> wrote: > > Hello Brian, > can you please run head -n 20 ../../scripts/ra/build/bin/ra and paste the output here? > > Best regards, > Robert > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALWv8VYQnE1Gscnvym79Qxf_n4YHvbijks5uz7XNgaJpZM4Y4n40>. >

[rvaser]

Hi Brian,
ra prints the assembly (constructed contigs) to stdout (i.e. you should have run it with python /home/brian/scripts/ra/build/bin/ra -t 32 -x pb pacbio_all.fasta > ra_assembly.fasta). File rala_assembly_graph.gfa is output from the layout stage in which the sequences are not polished (hopefully I will incorporate gfa into racon somehow soon). You should either re-run the whole pipeline or just polish the sequences from the gfa file manually (two iterations).

Best regards,
Robert