Hi guys,
I am running minia on two machine. One of them was killed during counting kmer. The machine is ~700GB memory and I have ITB disk for the output. The genome is human-size with 100x data. The data was trimed and error corrected. The last message of the log is "MB EXCEPTION: Pool allocation failed for 74 bytes (bank ids alloc). Current usage is 4154491796 and capacity is 4154491854". What is the problem? I tried three times, it is the same. I even recompile the minia.
The second one is a plant genome about 1,7GB, also with 100x. The data was trimed and error corrected. I used the kmergenie to find the best k, is 91 and the coverage cut-off is 1. But I run minia with default abundance-min, and the result is very bad. Should I set abundance-min to 1? And why the kmergenie suggest coverage cut-off is 1? Is it because all the preprocess I have done?
Thanks!
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Which version of Minia? Which version of KmerGenie?
See here, you probably want to increase min_abundance.
Given the error "Pool alloc.." reported, it is a newer version than in then previous link.
- How many input files did you give, is it a large number?
- Coverage cutoff of 1 is always going to give bad results, I recommend at least 2. Kmergenie may recommend 1 if it sees that the coverage is low. What do the kmergenie histograms look like?
Sorry, I haven't see the reply (new in biostar).
I am sure the number of input files is below 10.
But the sequencing coverage is more than 100. Is it caused by I keep all the short reads after trimming? Should I remove all the reads shorter than the recommend kmer?
Hi, sorry. I don't know my question have answer.
Minia is 2.0.3, Kmergenie is 1.6982.
I tried the default (2) and the one kmergenis suggested (1), both give me very bad results. The total length just cover half of the genome.