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voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
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Problem with big assembly #343

Closed ElsaMMendes closed 1 year ago

ElsaMMendes commented 1 year ago

I have problems with BIG assemblies with at least 750 million reads (with triplicates that's why it is big). Assemblies worked with also big assemblies with less reads (between 546 and 722 million reads)

I attached the log for the assembly of 750 million reads. log.zip

I ran it with maximum RAM : 550GB and --cpus-per-task=40 Here is the message from slurm: Slurm Job_id=26439056 Name=cap18 Failed, Run time 09:14:19, FAILED, ExitCode 249

SO IT IS NOT A OUT OF MEMORY ISSUE

I don't understand the problem because it worked with little kmers (so higher ressources requiered I think). It worked with an assembly of almost the same size ( 722 M).

ElsaMMendes commented 1 year ago

I solved the problem puting even more threads (50 instead of 40).