Error in mountain.bandpass_filter

[anniegott]

Hi,

I was wondering if any one could give me some advice with an error I have been receiving when trying to sort some of my datasets using mountainsort. The error I am receiving is:

**Warning problem reading 2d chunk in DiskReadMda32: 175440<>576000

PROCESS COMPLETED (exit code = 255): mountainsort.bandpass_filter
ERROR: Exit code is non-zero: mountainsort.bandpass_filter
Peak RAM: 1 MB. Peak CPU: 0%. Avg CPU: 0%. Elapsed time: 555.044 seconds.

2018-04-23:11-24-14-600 mp.main critical Error in mountainprocessmain "Exit code is non-zero: mountainsort.bandpass_filter"

mountainsort.bandpass_filter:: Critical: Error in process mountainsort.bandpass_filter MV4N6RB6NR9CWUIFIVJ7: Exit code is non-zero: mountainsort.bandpass_filter

Process finished: mountainsort.bandpass_filter

2018-04-23:11-24-15-882 mp.script_controller warning "Process returned with non-zero exit code: mountainsort.bandpass_filter"**

I have made space in the /tmp folder (2.2TB free).

Any ideas on how to fix this problem would be much appreciated!

Thanks,

Annie

[magland]

I am guessing you are running out of memory. but not sure. The newer version of the software (in pre-release now) will address this issue. But it is not quite ready for full sorting.

[magland]

Oh, actually, this could be a bug with the old version of numpy. Check on the docs for a command you can run to update numpy package.

[anniegott]

Thanks for getting back to me! I have tried running the sort on another Linux computer that I have configured mountainlab on, but am unfortunately getting exactly the same error. Apologies but I am very much a novice Linux user. I have searched in docs for commands on how to update numpy, however I cant seem to find them. Would you be able to direct me to them?

Thanks, Annie

[anniegott]

Alternatively - is there a way to run the program and not include the bandpass filtering stage?

[magland]

Hi Annie,
Could you please try the new version of the software? Still requires testing, but I think your issue will be resolved:

https://github.com/flatironinstitute/mountainlab-js

Jeremy

[magland]

Annie: note, the docs are not yet quite sufficient to do a full sort on your own data, buf if you run the example, it should be clear how to do it. I'm happy to help while we create the docs.