BWA MEM output directory

Question

[sarastrafella.ss]

hi everyone! I've a problem with output directory with bwa mem. this is my code for multiple fastq files:

for file in ./*.fastq;
do
    bwa mem hg19_index ${file} > ${file%.fastq}.sam
done

I want to put the output .sam files in another directory so I wrote:

for file in ./*.fastq;
do
    bwa mem hg19_index ${file} > path_to_output_directory/${file%.fastq}.sam
done

but it dosen't work! :( bwa mem puts the output files in the same directory of hg19_index files!

what is wrong? thank you!

[JC]

is your path a valid system path?

[sarastrafella.ss]

"path_to_output_directory" is the absolute path. I tried with with two or three files and it works

[sarastrafella.ss]

is it possible that bwa wants fastq and sam in the same folder?

[JC]

BWA uses the STDOUT stream, so the location is not defined by the program

[Joe]

It may not resolve the issue, but you should soft-quote your variables (" ").