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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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SqueezeMeta crashes when running on Ubuntu 22 virtualbox computer #774

Closed dutchscientist closed 5 months ago

dutchscientist commented 5 months ago

I am trying to run SqueezeMeta on virtualbox virtual computers, using up-todate Linux 22.04 with up to 14 cores and 98 GB of memory. These virtual computers run Mambaforge/Conda, and have had clean installs of SqueezeMeta in its own environment.

When running SqueezeMeta, we get regular crashes of the virtual computers with errors like: "The instruction at 0x00007FFBE3236DB2 references memory at 0x0000000000000000. The memory could not be written."

Has not happened before installing/using SqueezeMeta and they have been extensively and heavily used.

Will test the memory and try it on another computer, but any thoughts what this could be? Thanks :)

fpusan commented 5 months ago

That one is new to me. At what step of the pipeline is this happening? This seems to be related to virtualbox itself eg https://forums.virtualbox.org/viewtopic.php?t=100002 https://forums.virtualbox.org/viewtopic.php?t=102527 Not sure we can be of help with this...

dutchscientist commented 5 months ago

Thanks! Yes, I am beginning to think so as well, it's just that it never happened before on these virtual computers, even when they were stressed and all memory/processors used. Wil test further,, just wanted you to be aware and maybe others have the same.

It usually happens around step 4, even with the mock. Will try the --lowmem setting.

dutchscientist commented 5 months ago

It also starts crashing during file transfers now, so yes, I am afraid it is Virtualbox or the RAM itself.

I'll close it as it is not related to SqueezeMeta :)

fpusan commented 5 months ago

Glad to hear it's not my fault, and good luck solving that one out!

dutchscientist commented 5 months ago

Just to let you know, it was Virtualbox indeed. Moved to Hyper-V and it works absolutely fine. My co-worker is happy to start analyzing his data :)

fpusan commented 5 months ago

Good to know, glad it works now! :)