AV454 run: error message "Mempool 1 is reclaiming 96210 leaked bytes ..."

[Peter Pham]

Hi All,

Memory leak question:

I follow the README file and try to run AV454 with DATA=L3191 on my VM Linux box (memory = 3-4 GB).
I got the following warning message.  I wonder if this warning error will affect the result.  What is the requirement of system for AV454?

From the assemby log file, it took about 4 hours to finish run sample L3191.

elapsed time = 4:13:12, cpu time = 0.65sec, memory = 37Mb

Warning: Mempool 1 is reclaiming 96210 leaked bytes.
Warning: Mempool 2 is reclaiming 24556 leaked bytes.
Warning: Mempool 3 is reclaiming 52874 leaked bytes.
Warning: Mempool 5 is reclaiming 5 leaked bytes.
Warning: Mempool 7 is reclaiming 16 leaked bytes.
Warning: Mempool 9 is reclaiming 443 leaked bytes.
Warning: Mempool 11 is reclaiming 384 leaked bytes.
Warning: Mempool 13 is reclaiming 18 leaked bytes.
Warning: Mempool 15 is reclaiming 211 leaked bytes.
Warning: Mempool 17 is reclaiming 4179 leaked bytes.
Warning: There were 18 leaked mempools which were cleaned up at the end of the program run.
elapsed time = 0:00, cpu time = 0.05sec, memory = 11Mb

Thanks,
Peter

[Michael C. Zody]

Peter,

From this output, I don't see any evidence that the job failed to complete, or that the identified memory leaks are causing any errors in the assembly. Did you get output and does it look good?

The system requirements will vary extensively depending on the depth of coverage you attempt to assemble. In particular, we suggest that you don't try to assemble average coverage of more than about 250x using AV454. I believe there is now a downsampling routine included in the package, but it may be separate (I know we created one).

Unfortunately, the parent package of AV454, Arachne, is now minimally supported and the AV454 developer is no longer at Broad, so we are providing minimal support for this package going forward. I would suggest you try out our new assembler, Vicuna. It is primarily designed for Illumina data, but has a preprocessing module to allow it to handle 454 or unpaired Ion data as well. We find the performance on 454 data to be comparable to AV454, and the performance characteristics should be superior on less powerful hardware since, unlike Arachne, it was designed to be able to run on desktops.

Mike

[Peter Pham]

Mike,

Thanks for your suggestion.  I will try Vicuna.

Peter