Closed lelshura closed 1 month ago
Hello, This should be a bug from the bioconda version. If you installed from source, the executable is in the following folder ./bin/metaMDBG (in the build folder). So your command becomes: ./bin/metaMDBG gfa ./Scenario_1_concat_reads_metaMDBG 8 --contigpath --readpath
Fixed in v1.0
Hello, I am currently using metaMDBG for assembling metagenomic reads. I have encountered an issue where the unitigs.fasta.gz file is not generated during assembly. I have installed metaMDBG by building it from source using conda, following the instructions on the GitHub page.
I ran the following assembly command:
metaMDBG asm path/to/output_directory reads_concat.fq.gz -t 52
The process was completed successfully, and the contigs.fasta.gz file and tmp directory were generated. When looking into the tmp directory, each pass_k# subdirectory contains the assembly_graph.gfa, assembly_graph.gfa.unitigs, and parameters.gz files but no unitigs.fasta.gz file.
When I tried to run the metaMDBG gfa command
metaMDBG gfa assemblyDir k --contigpath --readpath
, I received the following error:
Could you please explain what might be causing this problem and how to generate the unitigs.fasta.gz file correctly?
Thank you