Permission denied

[RozemarijnVanDerPlaats]

Hey,
It is a very nice tool for making LAMP primers, but now I have a error and I don't know what was wrong. Maybe someone can help me to fix this.

First I tested the tool with a small genome with 30kb, also to check everything. Then I made a new bowtie database with other bacteria genomes. The output of Single was fine:
There ara 5843008 candidate primers used as F3/F2/B2/B3.
There are 3970570 candidate primers used as F1c/B1c.

Then was the goal to make specific primers for the detection:
perl par.pl --in xxx --ref /PATH/TO/GENOME.fna --common /PATH/TO/target-list.txt --bowtie /PATH/TO/GLAPD/bowtie --index /PATH/TO/GLAPD/bowtie/INDEX --left.
But then I goes wrong:
Now the program is handling the 1-th file, total files is 2...
Can't exec "/PATH/TO/GLAPD/bowtie": Permission denied at par.pl line 342.
Can't open the /PATH/TO//GLAPD/Inner/xxxxx-0.bowtie file!
The file in Inner doesn't exist, and which permission is denied?
I already checked the bowtie database and make a new one. I read in another issue about plasmids, so I also checked the genome of interest for chomosome sequence and plasmids, but that was only the chromosome.

So what is going wrong and what should be the solution?

[jiqingxiaoxi]

Hi,

In par.pl script, the "--bowtie" parameter points to the bowtie program, not its directory. So the right commond is "--bowtie /PATH/TO/GLAPD/bowtie/bowtie".

Best wishes!

[RozemarijnVanDerPlaats]

Hey

Thank you for the answer, that was the problem :)

Best wishes!