ERROR:reading

[This12]

I want to sketch my fasta file, but it have error massage by ERROR: reading filename.fasta. Can't I use fasta file? Or orther reason? (I use ./mash sketch -s 1000 -k 17 filename.fasta and ./mash sketch filename.fasta, didn't work)

[skoren]

Fasta files should be supported. You may need to provide the full path to the filename.fasta file (see issue #57). What does ls return in the directory you're running the command?

[This12]

Thank you for answer! But I use full path <./mash sketch /bip7_disk/shiyu106/mash-Linux64-v1.1.1/filename.fasta>, it still get ERROR: reading /bip7disk/shiyu106/mash-Linux64-v1.1.1/filename.fasta, and ls_ doesn't return me any files or orthers. The second question is ERROR: could not open /fullpath/genomic.fna.msh for writing(when I sketch), but I can sketch orther files in this directory. And the last question is that I want to know what's inside the RefSeqSketches.msh, is it have the all species, virus, fungi and something else? Thank you for help.

[ondovb]

RefseqSketches.msh is built on “refseq complete”, which contains genomes of all domains and plasmids. To help with the other errors, could you paste in the exact commands along with the output of “ls”?

[This12]

Thank you for answer! But I am not really sure what is ls ...... , is the command to view the files of directory?

[ondovb]

Exactly, just so we can see the context. A screen grab of the terminal window could also be useful if you don't mind sharing.

[This12]

Sorry I'm late for reply, the first picture is first question, the second picture is second question, and both of them are not create or return any files...

[ondovb]

That looks fine. You may need to go to your system administrator for this, as I think it is likely a permissions problem or other issue beyond Mash.

[This12]

OK, I will keep trying. Thank for your help!