Some problem about running KMC3, error: Cannot open temporary file tmp/kmc

Some problem about running KMC3, error: Cannot open temporary file tmp/kmc_00000.bin

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6.2 years ago

niuyy9026 • 0

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 • 2.0k views

ADD COMMENT • link 6.2 years ago by niuyy9026 • 0

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

ADD REPLY • link 6.2 years ago by WouterDeCoster 47k

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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 REPLY • link 6.2 years ago by niuyy9026 • 0

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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?