minimap2 doesn't work

[avitalsteiman]

Hi, I installed pomaxis and am running mini_align in the pomaxis setting, but for some reason it does not recognize the minimap2 command.

I run:

mini_align -i filtered.fq -r ~/refs/lambda_ref.fasta -P -p lambda -t 14

I get this error: /home/biomesh/git/pomoxis/venv/bin/mini_align: line 95: minimap2: command not found

Also, if i try to run minimap2 directly using the command:

../../../git/pomoxis/submodules/minimap2-2.14/minimap2 -x map-ont -t 14 -a /home/biomesh/refs/lambda_ref.fasta.mmi filtered.fq I get : Segmentation fault (core dumped)

I noticed that minimap2 was already downloaded but not installed by another user on the computer i'm running on, but even after i erased the file it doesn't work. "Minimap" is installed though. Could this be part of the problem.

Thanks, Avital

[cjw85]

Hi @avitalsteiman,

From your second error it appears the installation successfully compiled minimap2, whilst the first error suggests the program was not move correctly to a location where mini_align can find it: minimap2 should be present under /home/biomesh/git/pomoxis/venv/bin/. Can you confirm the contents of this directory? It you have a log file from when pomoxis was installed this would be useful; if not perhaps try a clean install with e.g.:

git clone --recursive https://github.com/nanoporetech/pomoxis pomoxis_clean
cd pomoxis_clean
make install &> install.log

and attach the file install.log to this issue.

For the Segmentation fault in the second error, can you confirm that the error does not occur for your inputs with a minimap2 compiled independently of pomoxis?

[avitalsteiman]

Thanks for your response.

I checked and minimap2 was missing from "/home/biomesh/git/pomoxis/venv/bin/" I re-installed pomoxis using the commands you included. The install.log is attached. I then re-ran the mini_align command: mini_align -i filtered.fq -r ~/refs/lambda_ref.fasta -P -p lambda -t 14 and received this output on the screen:

-P option is deprecated Found minimap files.

In the end I erased the file ~/refs/lambda_ref.fasta.mmi that already existed and noticed that there was also a problem with the file ~/refs/lambda_ref.fasta so i replaced it with the correct file and everything ran.

So thank you for your help. Avital

install.log

[cjw85]

Aside from the python3.7 errors (see https://github.com/nanoporetech/pomoxis/issues/25, python3.7 is unsupported, the next release will make this more clear), there does not appear to be anything untoward going on during installation.

You say mini_align created a test.sam file, however this is not a file that would be created given the command you say you have run. I suspect the minimap index (lambda_ref.fasta.mmi) is somehow invalid, causing the segmentation fault. Could you attach your ~/refs/lambda_ref.fasta?

[avitalsteiman]

Hi, I updated my post at the same time that you responded.... Your assessment was correct. I noticed that in fact there was a problem with the originl lambda_ref.fasta file and the .mmi file. After I replaced the lambda_ref.fasta file and removed the lambda_ref.fasta.mmi file the mini_align command worked.

Thanks for your help. I appreciate your quick response. Avital

On Mon, Jan 14, 2019 at 4:12 PM cjw85 notifications@github.com wrote:

Aside from the python3.7 errors (see #25 https://github.com/nanoporetech/pomoxis/issues/25, python3.7 is unsupported, the next release will make this more clear), there does not appear to be anything untoward going on during installation.

You say mini_align created a test.sam file, however this is not a file that would be created given the command you say you have run. I suspect the minimap index (lambda_ref.fasta.mmi) is somehow invalid, causing the segmentation fault. Could you attach your ~/refs/lambda_ref.fasta?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nanoporetech/pomoxis/issues/26#issuecomment-454017734, or mute the thread https://github.com/notifications/unsubscribe-auth/Ase1xwsYkJs2ndudOuvRFTk2RlH1i5pMks5vDJA6gaJpZM4Z9Bga .

[cjw85]

No problem, happy to help.