Error opening params file about dicey

[tobiasrausch]

Have you installed dicey using bioconda? The primer3 config directory is only included in the source code. Please also check that the config files are really present in that directory, i.e.:

ls $config/tetraloop.dh

[AlexGaithuma]

I compiled from the source and tetraloop.dh file is present.

[tobiasrausch]

Thanks. Sorry I haven't seen this earlier but you use a custom reference (../18S_All.fasta primers.fa). You need to index this reference first as described in the README because dicey is designed to work across entire, large genomes. For model organisms and human you can also download the pre-indexed genomes here. To run the example, you would simply download all Homo_sapiens.GRCh37.dna.primary_assembly.fa* files and then:

dicey search -c 45 -l 1000 -g Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz -i /media/bioadmin/24e12c01-7941-49f5-9647-eeebabd15082/packages/dicey/src/primer3_config/ primers.fa

The config directory also needs a '/' at the end.

[AlexGaithuma]

Thanks.
I had ran the indexing but no index file was generated.
The problem was fixed by compressing the reference fasta file to .gz format.

Now everything works

[AlexGaithuma]

I still get the error

Error opening params file

even with the indexing

[tobiasrausch]

Have you added the slash '/' at the end of the directory? Can you post the command?

[AlexGaithuma]

Thanks.
It now works.