path error

Question

[mariana.ferrera]

Hi everyone

Im tryinng to run the populations module of stacks but im getting this error " Failed to open '/stacks/pop_534/populations.log' for writing"

my script;

populations -P $PWD/stacks/m5M3n4_denovo_mrf --popmap ./popmap_mrf.txt -O /stacks/pop_534  -p 1 -r 0.8 --min-maf 0.05 --fasta-samples --fasta-loci --vcf --genepop ---write-single-snp --threads 3

pwd: /home/mariana/libreria/rawdata/radtags01

input data directory - P: /home/mariana/libreria/rawdata/radtags01/stacks/m5M3n4_denovo_mrf

output data -O : /home/mariana/libreria/rawdata/radtags01/stacks/pop_534

popmap : is in pwd so i only put ./popmap_mrf.txt

Thanks in advance

Mariana

Answer 1

[rfran010]

It looks like you have an absolute path where I think you want a relative path?

  -O ./stacks/pop_534

[mariana.ferrera]

oh thanks i added the dot and it run :D

[Pierre Lindenbaum]

validate the answer by clicking on the check mark on the left please