System(mv) command problem

Hi,

I’m new with mothur. When I try to do the system(mv) command in the MiSeq Sop I have a problem “No such file or directory”.
Is anybody had the same problem ?

I have a MacBooK Pro late 2011.

This is the problematic commands:
mothur > system(mv silva.bacteria.pcr.fasta silva.v4.fasta)
mothur > system(mv stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.shared stability.an.shared)
mothur > system(mv stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.0.03.cons.taxonomy stability.an.cons.taxonomy)

Thank’s!

Max

If you do system(ls) do you see the files you are trying to move?

Hi Pat,

I have the same problem with the system(mv) command. I did system(ls), but did not see the files I’m trying to move. What does this mean, and how to solve it?

Thanks,
Soon

Do you have a mac, linux, or windows computer? If you want to see the contents of the folder you are in, you need to do system(ls) [for mac/linux]or system(dir) [for windows].

Pat

Hi Pat,

I’m using mac and windows, and having the same problem for both. I think the problem is due to the files I’m renaming are not in the mothur folder. Is it possible to rename files located in other folders? I tried listing the full path of the files but “The syntax of the command is incorrect.” appeared.

Thanks,
Soon

The files have to be in the same folder that you are running mothur from.

Pat

Hi,

Thank’s for your help. I have a mac.

I tried to do system(ls), but it gives me:

mothur > system(ls silva.bacteria.pcr.fasta silva.v3v4.fasta)
ls: silva.bacteria.pcr.fasta: No such file or directory
ls: silva.v3v4.fasta: No such file or directory

And system(mv), gives me:

mothur > system(mv silva.bacteria.pcr.fasta silva.v3v4.fasta)
mv: rename silva.bacteria.pcr.fasta to silva.v3v4.fasta: No such file or directory

Thank’s
Max

Perhaps we can just rename it manually ?

Max

Max,

You aren’t in the correct folder. Run system(ls) from the mothur prompt.

Pat