This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Some problem about running KMC3, error: Cannot open temporary file tmp/kmc_00000.bin

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
• 2,821 views • link
written by niuyy9026 • niuyy9026

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

• 0 views • link
written by WouterDeCoster WouterDeCoster

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.

• 0 views • link
written by niuyy9026 • niuyy9026

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?

• 0 views • link
written by niuyy9026 • niuyy9026

0 answers

No answers yet.

Log in to answer this question.

More posts like this