Question: Soapdenovo .Kmerfreq File Error
gravatar for mariekuh123
6.1 years ago by
mariekuh1230 wrote:

Hi, I try to run SOAPdenovo on a linux server with the following command: ./SOAPdenovo all -s 2691.config -K 63 -R -o 2691

The contents of config file are: max_rd_len=150, [LIB], avg_ins=200, reverse_seq=0, asm_flags=3, rd_len_cutoff=100, map_len=32, q1=/path/file, q2=/path/file

When I run the command, the program reads the files and will make a pregraph, but then there is an error: Can't open *.kmerFreq

I can't find any solution on the internet, I have tried other parameters and other files but the error still appears.

Can somebody help me with this problem?

error • 2.3k views
ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by mariekuh1230

Is there a *.kmerFreq file in the working directory after the program dies? If not, the program may be running out of memory trying to generate this data.

ADD REPLYlink written 6.1 years ago by SES8.2k

Try to run it step by step. first pregraph, then contig, then map, then scaff.

ADD REPLYlink written 6.1 years ago by Buttonwood40
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