Neng Huang
Neng Huang
Hi @estolle, The output file ```full_table.tsv``` may give the information you need which includes the region in the genome hits the single copy gene.
Hi @arslan9732, It's interesting. Could you share the protein file and also which lineage do you use? So I can figure out what happened. Thanks!
Thank you for the suggestion! Too many output files may cause IO problem. I will add the feature.
Hi @larsmoret Could you list the files (also the filesize) under the directory "fungi_odb10" of output folder?
Hi @katiecdillon Thanks for providing the script. Could you specify a different output folder name for each input assembly, instead of using "$D2" for all the assemblies?
Hi @larsmoret @katiecdillon , I have added some checks in the code to understand why something went wrong. The reason for KeyError "Target_species" is that there is no candidate alignment...
To @larsmoret The error "failed to open/build the index" is reported in miniprot. You can test the alignment manually by "miniprot --trans -u -I --outs=0.95 -t 20 --gff ~/finalassemblies/CBS1922.fasta mb_downloads/fungi_odb10/refseq_db.faa.gz...
Hi @larsmoret, All BUSCO genes are missing is because that there is no gene can be aligned to the assembly and pass the BUSCO's threshold, which means the genes are...
Hi @shelkmike, Thanks for the information, I will update it as soon as possible. Neng
Hi @aabaricalla Yes, very good suggestion, it will be integrated into the next version. Thanks so much! Neng