Taxonomy2function java error: Too many open files

Bug Reports
1

Hi, when using taxonomy2function (-mro) with the MEGAN Ultimate version 6.24.15 the job is cancelled and I get java error: Too many open files

I have a total of 44 .daa files in the directory that I run taxonomy2function:

taxonomy2function -i *.daa -o taxonomy2function.txt -a Taxonomy -b KEGG -af path -bf path -l counts -s tab -au true -bu false -sh true -ps semi-colon -mro

The error comes when analyzing the third file at step:

Processing: Second classification
10% 20% 30% 40% 50% 60% 70% 80% 90% Caught:
java.io.FileNotFoundException: sample3.daa (Too many open files)

2

I took a look at this, but it is not obvious what the problem is. As a work around, run the program multiple times, using a smaller number of files per run.

3

I can do that and that is a good workaround, it is also faster (i.e. one file per job).

Is there an easy way to then merge all the output files (as the taxonomy2function already does this)?

4

The tools/compute-comparison program can take multiple files and create a comparison file for them.

5

As I understand the compute-comparison tool only works with daa or rma files.

After running taxonomy2function I will get one .txt per sample. These txt files need to be merged to one joint table. Taxonomy2 function does this already when l being run as one command on multiple samples, but now gives the java error.

The function to join the tables was added in version 21.16: Taxonomy2function suggestions - #2 by Daniel

But i am not sure how this is done if i run each sample separately using taxonomy2 function.

6

Sorry, you are right. Compute-comparison is not the tool that you want.

I will take another look at the code to try and figure out why the “Too many open files” error occurs.

I ran the program on 50 files with no problems on my laptop. So, I’m wondering whether you ran program on a server that was also busy with other jobs?

7

After I remove -mro from my command line it works. So the Java error “Too many open files” definitely has something to do with -mro.