I am currently trying to run the Miseq SOP exemple with some of my samples for a practical course I’m preparing.
I’m working on my lab’s computing cluster and the files required for MiSeq SOP (silva.bacteria and trainset9 files) are downloaded to a specific directory which can’t be my working directory.
Anyway, everything works up to the “classify.seqs” command line:
mothur > classify.seqs(fasta=/home/user/r/rpeguilhan/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta, count=/home/user/r/rpeguilhan/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.count_table, reference=/opt/cluster/contrib/apps/anaconda/3/envs/trainset9_032012.pds.fasta, taxonomy=/opt/cluster/contrib/apps/anaconda/3/envs/trainset9_032012.pds.tax) Using 12 processors. Generating search database... [ERROR]: Could not open /opt/cluster/contrib/apps/anaconda/3/envs/trainset9_032012.pds.8mer DONE. It took 11 seconds generate search database. Reading in the /opt/cluster/contrib/apps/anaconda/3/envs/trainset9_032012.pds.tax taxonomy... [ERROR]: Could not open /opt/cluster/contrib/apps/anaconda/3/envs/trainset9_032012.pds.tree.sum DONE. Calculating template taxonomy tree... [ERROR]: Could not open /opt/cluster/contrib/apps/anaconda/3/envs/trainset9_032012.pds.tree.train DONE. Calculating template probabilities... [ERROR]: Could not open /opt/cluster/contrib/apps/anaconda/3/envs/trainset9_032012.pds.trainset9_032012.pds.8mer.prob [ERROR]: Could not open /opt/cluster/contrib/apps/anaconda/3/envs/trainset9_032012.pds.trainset9_032012.pds.8mer.numNonZero DONE. It took 17 seconds get probabilities. Classifying sequences from /home/user/r/rpeguilhan/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta ... Mismatch with taxonomy and template files. Cannot continue. Mismatch with taxonomy and template files. Cannot continue.
I tried to change my input and output directories with the command line set.dir but nothings helped. It seems that mothur can’t find the temporary files… but I don’t know what to do.
Can anyone help me?