System(mv) command problem

Commands in mothur
#1

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

#2

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

#3

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

#4

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

#5

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

#6

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

Pat

#7

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

#8

Perhaps we can just rename it manually ?

Max

#9

Max,

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

Pat