rvaser
Minimap2 will not run
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
Hello Brian,
can you please run head -n 20 ../../scripts/ra/build/bin/ra and paste the output here?
Best regards, Robert
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 [email protected] 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 https://github.com/rvaser/ra/issues/5#issuecomment-442782496, or mute the thread https://github.com/notifications/unsubscribe-auth/ALWv8VYQnE1Gscnvym79Qxf_n4YHvbijks5uz7XNgaJpZM4Y4n40.
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
On Nov 29, 2018, at 8:06 AM, Brian-Tyler St.Hilaire [email protected] 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 <[email protected] mailto:[email protected]> 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 https://github.com/rvaser/ra/issues/5#issuecomment-442782496, or mute the thread https://github.com/notifications/unsubscribe-auth/ALWv8VYQnE1Gscnvym79Qxf_n4YHvbijks5uz7XNgaJpZM4Y4n40.
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