make.contigs error

Hi all,

I’m trying to run make.contigs on my dataset, but got the following error:

_mothur > make.contigs(file=stability.txt)

Using 1 processors.
Unable to open A003-H7-GAGATAAC-Rowe-run20151230R_S1_L001_R1_001.fastq. Trying default /appl/molbio/mothur/mothur.1.36.1/A003-H7-GAGATAAC-Rowe-run20151230R_S1_L001_R1_001.fastq
[WARNING]: can’t find /appl/molbio/mothur/mothur.1.36.1/A003-H7-GAGATAAC-Rowe-run20151230R_S1_L001_R1_001.fastq, ignoring pair._

Apparently this is shown for all the samples (I haven’t checked it all, but it seems the case). What could be going on? Could it be something wrong from the fastq. files?



If you run ls (mac/linux) or dir (windows) from the folder where you are running mothur do you see the fastq files?


I’m using a supercluster computing system (CSC, Taito) as a host from a Mac as local computer. The command works when run from my local computer, but it does not from that host. I’ve already made sure that Mothur actually works from such a host (running other commands), so I’m a bit stuck here.


Hi again,

Apparently I fixed the problem. You were right in your suggestion: the fastq files were not properly uploaded into the directory. Now the analysis is running.
Many thanks,