Running out of memory from performing isoform discovery and quantification under low-memory mode

[chingyinwan]

Hello. I am trying to use Bambu v3.8.0 to perform isoform discovery and quantification on 8 BAM files with sizes ranging from 30 GB to 52 GB. The server I am running Bambu on has 256 GB of memory. However, the Bambu process ran out of memory even under its low-memory mode. The log messages I got before it crashed are as follows:

--- Start generating read class files ---
< warning messages not included here >
--- Start extending annotations ---
Using a novel discovery rate (NDR) of: 0.47
--- Start isoform quantification ---

Running journalctl -rx, I see an Out of memory: Killed process... log message.

I am calling bambu() with all 8 BAMs passed into it and with quant = TRUE, discovery = TRUE and lowMemory = TRUE. The BAMs only contain primary alignments and contain no secondary or supplementary alignments. What can I do to optimize Bambu's memory usage?

Thank you!

[abcdtree]

I have similar problem. I have bam files with 380G and assigned 800G RAM for the process. I found the step makes the program to crash is actually the output step.

I am trying to output novel transcript only to see whether it can help.

@chingyinwan Please let me whether you have already found some solution.

Thanks