Error running bismark_genome_preparation

[chrismahony]

I am running:

bismark_genome_preparation --path_to_aligner /my_path/bowtie2-2.5.0-mingw-x86_64/bowtie2-2.5.0-mingw-x86_64/ --verbose /my_path/RRBS/

And I get the following output just after step III launches:

bowtie2-build-s does not exist, try running `[g]make bowtie2-build-s' Parent process: Failed to build index

Could you help?

Thanks Chris

[FelixKrueger]

Hmm, not exactly sure what this is. Does Bowtie2 itself run fine? You could test this by moving into the Bisulfite_Genome/CT_conversion/ folder, and then run something like:

bowtie2-build --verbose genome_mfa.CT_conversion.fa BS_CT

[chrismahony]

This works fine, I also run this for the GA and it runs fine.

I run:

module load Bowtie2/2.4.4-GCC-10.3.0 bowtie2-build --verbose genome_mfa.CT_conversion.fa BS_CT

Can I manually run the next steps of creating the genome in a similar way?

Thanks Chris

[FelixKrueger]

Hi Chris,

Yes, you should be able to just execute this step once for the CT_conversion and once for the GA_conversion folders. I still don't quite understand where the error comes from. Maybe it is because of different versions of Bowtie2 you used for the Bismark and manual way?

[chrismahony]

OK great, how do I get bismark to start after this step?

Thanks Chris

[FelixKrueger]

Bismark should just work normally, just point it to the correct folder

bismark --genome /my_path/RRBS/  file_trimmed.fq.gz

or something similar.