imgag/ClinCNV

Error in writeLines [...] cannot open the connection

Closed this issue · 3 comments

frmacomber commented

Hi ClinCNV developers,

running ClinCNV with the provided test data produced an error which we couldn't resolve. All packages are installed as indicated (install_deps_clincnv.R).

log.txt

Thanks a lot!
Best
PS: running on HPC w/ ubuntu 18.04.5.

GermanDemidov commented

Hi frmacomber,

seems that the tool actually worked, 2 samples were analyzed (can you check that the results for the first 2 samples make sense?). For the 3rd patient it looks that the tool could not write to the file, "cannot open the connection" basically means that there was a system error, not sure, the file was removed in the middle? does this file already exists and have no permission to overwrite?

It could be an error of the tool, but the log says that there was an error in writeLines which is an R function, and cannot open the connection indicates that the file is not available.

Overall the log looks a bit strange - no probes were filtered out due to extreme GC/low coverage...Is it a very short targeted panel?

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frmacomber commented

Hi German,
thanks for the quick reply.
In the results folder, I find the ontargetNormal.summary.xls file, which has 49 lines with values for noises and avgDepth. The clusteringSolution.png file is there and looks fine. Also, there is the folder normal containing folders 0 to 4, all empty.

There is no pre-existing file. When running the test data set provided on github, that is what we get. I have no idea why it aborts at the 3rd sample.
Regarding the GC coverage - that should not be an issue with the test data I think.

Thanks again for the quick response and have a nice weekend.

GermanDemidov commented

Hi frmacomber,

that's fine, I am at work =) yes, the test was generated in this way, so now it is all clear. But the folders should not be empty. There should be 3 files per sample. However I doubt this is the problem of the tool. We use test data as a part of continuous integration and CNV calling in these 50 samples is checked each time we commit anything.

https://travis-ci.org/github/imgag/ClinCNV - this is the result, and this https://travis-ci.org/github/imgag/ClinCNV/jobs/756566778/config is the config - could you check that you run more or less similar command?

Have a nice weekend too!

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