Question: Some problem about running KMC3, error: Cannot open temporary file tmp/kmc_00000.bin
0
gravatar for niuyy9026
13 months ago by
niuyy90260
niuyy90260 wrote:

I tried to run the KMC3 in Linux. After make, I tried to run the kmc by the command line: /home/niu/KMC-3.0.1/bin/kmc -k20 reads.fq kmers1 tmp. I got the error messages as Error: Cannot open temporary file tmp/kmc_00000.bin. Could anyone help me to fix this problem? Many thanks.

software error • 577 views
ADD COMMENTlink written 13 months ago by niuyy90260
1

Try a full path to a tmp folder. /tmp/ or in your own home directory ~/tmp/ (make sure the folder exists).

ADD REPLYlink written 13 months ago by WouterDeCoster38k

Thanks for your response. I solved the problem by using the example command line in KMC2 supplementary file instead of KMC3 knc_tool pdf. The command line is something like kmc -k27 -m24 NA19238.fastq NA.res \data\kmc tmp dir. I don't know why, but it works. Anyway, thanks again for your response.

ADD REPLYlink written 13 months ago by niuyy90260

Oh, I finally understand your meaning. If I just create a folder and name it tmp, Then it works. By the way, have you ever tried to use this Program?

ADD REPLYlink written 13 months ago by niuyy90260

No never heard of it

ADD REPLYlink written 13 months ago by WouterDeCoster38k
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