Stacks: Unable to open log file 'home/mdominguez/ref_map/prueba_md/ref_map.log'; No such file or directory

Question

[dominguez.matias]

Hi everyone!

I am new in Biostars! I have problems with stacks to run the pipeline ref_map.pl. I run my code:

ref_map.pl -o home/mdominguez/ref_map/prueba_md/results -m 3 -b 1 -s M1.sorted.bam -s M2.sorted.bam -s M3.sorted.bam -s M4.sorted.bam -s M5.sorted.bam -s M6.sorted.bam -s M7.sorted.bam -s M8.sorted.bam -s M9.sorted.bam -s M10.sorted.bam -s M11.sorted.bam -s M12.sorted.bam -s M13.sorted.bam -s M14.sorted.bam -s M15.sorted.bam -s M16.sorted.bam -s M17.sorted.bam -s M18.sorted.bam -s M19.sorted.bam -s M20.sorted.bam -s M21.sorted.bam -s M22.sorted.bam -s M23.sorted.bam -s M24.sorted.bam  -s M25.sorted.bam -s M26.sorted.bam -S

And then I received this message: Unable to open log file 'home/mdominguez/ref_map/prueba_md/ref_map.log'; No such file or directory

Anyone have an idea about this kind of error?

Many thanks!!

Matías Dominguez National Institute for Agriculture Research Argentina

[dominguez.matias]

Many thanks Mensur Dlakic!! In fact that was the mistake, I was breaking my head and it was so simple. Thank you so much for your help.

Kind regards,

Matías

[GenoMax]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

[Kevin Blighe]

No te preocupes Matias.

Answer 1

[Mensur Dlakic]

It depends in which directory you are when running this command, and also if you are trying to create a directory.

Most likely you are forgetting to put / in front of home so it should be:

-o /home/mdominguez/ref_map/prueba_md/results

Or if you want to actually store your output in a sub-directory called home/mdominguez/ref_map/prueba_md that is inside your present directory, before entering your command you need to do:

mkdir -p home/mdominguez/ref_map/prueba_md

Chances are you are simply forgetting to type /.