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rkajitani / MetaPlatanus

De novo metagenome assembler
GNU General Public License v3.0
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Error: contig_assembly error! Function not implemented #7

Closed Krasnopeev closed 2 years ago

Krasnopeev commented 2 years ago

Hi!

MetaPlatanus was installed with conda as described in manual without any issues.

I used PE 2x200bp Illumina reads and run ended with error. Here is log file content:

Error: contig_assembly error!
Function not implemented

used command:

metaplatanus -IP1 BFR_R1_paired.fq BFR_R2_paired.fq -o metaplat_out -t 10 >log.txt 2>&1

also here is log file from folder metaplat_out_intermediate metaplat_out.assembleLog.txt

How to resolve it? Thanks!

rkajitani commented 2 years ago

Thank you for reporting. Unfortunately, MetaPlatanus requires more memory than it could use. A memory limit can be specified by -m option (default, 0.75 * available_memory), and MetaPlatanus used "-m 18.75" in your environment. So, more memory (RAM) amount may be needed to finish the assembly of your data. A larger value of "-min_cov_contig" option will reduce the memory usage, but the size of the resulting assembly will also decrease. I'm sorry to bother you.

Krasnopeev commented 2 years ago

Oh, ok! I will try with different memory options. thanks!