mvaudel
commented
11 months ago Hi Magnus and thanks for the detailed report.
I am afraid you are not doing anything wrong. It seems that spectrum files are too large and our index runs out of capacity. A short-term fix is to split the spectrum files - the easiest for this is to convert them to mgf and then split the files. I am working on a generic fix but that will take a bit more time.
One thing that I was wondering also is whether these are DIA files? SearchGUI is made to handle DDA files, I am not sure how Tide handles DIA.
Hope it helps,
Marc
hbarsnes
Hello, I have a set of files n=12 for my full set of spectra and n=6 for one condition (part of the full set). I am working with Searchgui v. 4.2.17 installed via conda (see yml for environment information - searchgui_environment_yml.txt)
As I am running on a linux based machine, I am running searchgui through the command-line interface. I have tried running searchgui with my full set of files, n=12, but get this Error: 'File exceeds memory mapped reader max buffer size.' (full output - full_set_output.txt). When running with only one condition, n=6 files, I get the exact same error (one_condition_error.txt). I have tried to increase the memory allocated to the Java Virtual Machine, however this is fairly finicky in conda and does not seem to solve the problem (if the way I do it work). What is even more stange and raised my eyebrows is the fact that searchgui seem to 'run out of memory' at n-1 files in both instances, both for the full set of files and for one condition.
Any explanation on why this may be or wrongdoing on my part?
Cheers, Magnus