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nanoporetech / ont-assembly-polish

ONT assembly and Illumina polishing pipeline
Mozilla Public License 2.0
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update in analysis.mk #21

Closed fabiodepa closed 5 years ago

fabiodepa commented 5 years ago

line 62: the -o option of samtools sort will print the sorted bam file in the stdout so I removed it and let only the prefix for the bam file name, samtools sort withount the -o will add the .bam suffinx to the indicated file name.

bsipos commented 5 years ago

Are you using by any chance a very old version of samtools? It should work fine with the latest versions.

fabiodepa commented 5 years ago

I am using the docker container build from the Dokerfile in the GitHub. I get the bam on stdout while running the pipeline within the doker container, that's why I think that -o could be the problem.

bsipos commented 5 years ago

I see. I have updated the docker image base to latest Ubuntu LTS. Could you build and image and check if it solves the problem?

fabiodepa commented 5 years ago

Hi @bsipos I tried to do as you suggest rebuilding the docker but it get stucked at some point asking for geographic area... I do not know how to escape from that point. I suppose is a Ubuntu LTS request...

btw this was my first pull request to an existing project on GitHub, I hope I did it the right way...

bsipos commented 5 years ago

Hi @fabiodepa

Thanks for the pull request! It is useful for me to know about this issues. I have pushed out some changes which should fix the apt-get issue. Could you pleas try to build the image again?

Botond

fabiodepa commented 5 years ago

Hi @bsipos Sorry for the delay. I attach here the stdout and stderr of the building of the new Dockerfile. I had to compile the Dockerfile on a Ubuntu 16.04 LTS because at the moment my Ubuntu 18.04 workstation is out of service... Do you think this could be the porblem?

stderr.txt stdout.txt

Fabio

bsipos commented 5 years ago

The problem was that the JRE install package I was using is no longer supported. Pushed out a fix, please try building again.

Botond

bsipos commented 5 years ago

Hey @fabiodepa ! Does this work for you now?

fabiodepa commented 5 years ago

hi @bsipos ! Sorry for the delay... Yes, it works now both the installation and the pipeline, no errors at all! I think I can close this pull request, correct? Thanks!