I desperatly try to execute my batch file with mothur but it does not recognize my environmental variable
my batch file is written like that:
#CONTIGS_PARAMETERS
OLIGO=./lbe.16S.V1V3.oligos.txt
PDIFFS_CONTIGS=2
PROCESSORS_CONTIGS=16
#STEP 1 : CONTIGS…
make.contigs(file=fastq.files.table, oligos=$OLIGOS, pdiffs=$PDIFFS_CONTIGS, processors=$PROCESSORS_CONTIGS)
summary.seqs()
and the error is :
mothur > OLIGO=./lbe.16S.V1V3.oligos.txt
[ERROR]: You are missing (
[ERROR]: Invalid.
mothur > PDIFFS_CONTIGS=2
[ERROR]: You are missing (
[ERROR]: Invalid.
mothur > PROCESSORS_CONTIGS=16
[ERROR]: You are missing (
[ERROR]: Invalid.
mothur > make.contigs(file=fastq.files.table, oligos=$OLIGOS, pdiffs=$PDIFFS_CONTIGS, processors=$PROCESSORS_CONTIGS)
Unable to open $OLIGOS. Trying default /work/fake/scripts/mothur-1.43.0/$OLIGOS.
Unable to open /work/fake/scripts/mothur-1.43.0/$OLIGOS. Trying mothur’s executable location /work/fake/scripts/mothur-1.43.0/$OLIGOS.
Unable to open /work/fake/scripts/mothur-1.43.0/$OLIGOS.
Unable to open $OLIGOS
[ERROR]: $PROCESSORS_CONTIGS is not an integer. Setting processors to 64
[ERROR]: cannot convert $PROCESSORS_CONTIGS to an integer.
[ERROR]: cannot convert $PDIFFS_CONTIGS to an integer.
[ERROR]: did not complete make.contigs.
It’s look like it’s trying to open litteraly $OLIGO and the other variables
I have not so many documentation about environmental variable in mothur
i have already tried all of this link : https://www.mothur.org/wiki/Batch_mode with no sucess
Thanks for your Help
