Closed ronald-jaepel closed 8 years ago
Also fixed by https://github.com/Phelimb/atlas/commit/ef6a4a9f3b90a8dd1e995140bdf9d8993690d87f (v0.3.11) . I think a similar issue occurs as in #13 at the point of the very low coverage kmers.
@ronald-jaepel How easy would it be for you to rerun all of these analyses?
I should be able to do that today.
did you change the output .json format?
Same situation as in Issue #13
but this time walk picked an allele that has one additional mutation compared to the original:
Repeat of the debugging locations: The genomes, reads and graphs can be found at:
/data1/projects/ronald_jaepel/atlas_test/Simulation_Products/generated_genomes/2016_05_09_1252/ecoli_K12_MG1655ref.fa
/data1/projects/ronald_jaepel/atlas_test/Simulation_Products/simulated_reads/2016_05_09_1252/ecoli_1.fq.gz or ./ecoli_2.fq.gz
/data1/projects/ronald_jaepel/atlas_test/Simulation_Products/simulated_graphs/2016_05_091252/ecoli.k31.ctx (e.g. ecoli_tem183.k31.ctx)
The databases used are: databases.zip where gn_amr-genesmutated.fasta was used to generate the genomes, reads and graphs while gn_amr-genes.fasta was used as panel for walk
The JSONS output of the atlas runs can be found at: /data1/projects/ronald_jaepel/atlas_test/JSONS/2016_05_09_1252/