Entering edit mode
11.2 years ago
mariekuh123
•
0
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?
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.
Try to run it step by step. first pregraph, then contig, then map, then scaff.