Christophe Klopp

I've aligned 559 contigs smaller than 100kb on NR (diamond blastx) and 451 had proteic hits which all come from species phylogenetically related to the assembled species.

Hi, The configuration path can be set in the application.properties file : https://github.com/genotoul-bioinfo/dgenies/blob/master/application.properties entry => config_dir = ###USER###/.dgenies Can you use this to set the directory?

Yes you're right. You could try adding the location ($PATH_TO_CONDA_ENV/lib/python3.6/site-packages/etc/dgenies/) in the config_file_search array which is located at line 23 of src/dgenies/config_reader.py using os.environ["PATH_TO_CONDA_ENV"]+"/lib/python3.6/site-packages/etc/dgenies/application.properties".

We have replaced iteritems by items in the code and it worked. Here is a link a data subset including fasta and both gff files : http://genoweb.toulouse.inra.fr/~klopp/tmp/chr1.tgz and the command...

Hi, I have the same error or kind of error, after 4 hours ... 03:06:01 5Gb INFO: Export to GFA and compressed contigs 03:06:58 5.7Gb INFO: Finished repeat resolution 03:07:07...

No sorry, it is not my data and it is was just to test your code. We already have a good assembly for it with hifiasm.

Hi, In our database I see all these jobs (job IDs) which were ran successfully : exi_target_coe_query exi_target_kan_query coe_target_kan_query exi_target_coe_query_2 exi_target_kan_query_2 coe_target_kan_query_2 kan_target_exi_query coe_target_exi_query kan_target_coe_query coe_target_exi12_query Shh6C_20240103220832 zwr77_20240104010108 l9U1A_20240104190219 Some...

Hi, Thank you for you answer. If you do not want to parse non standard file formats, the option could be to use a parameter string 'scaffold1:start1-end1,scaffold2:start2-end2,..,' The other use...

Here is the link to my log file [LJA.log](https://genoweb.toulouse.inra.fr/~klopp/tmp/LJA.log)

Yes, I work with exact kmers because I'm interested in locating kmer found a low number of times in the genome. They are tens of millions of them and therefore...