SolayMane

for your first question : imagine that your output dir has the name workdir: ````bash for file in $(find workdir -type f -name "snps.*");\ do name=$(echo $file | cut -d"/"...

I want to extract the genes from the query sequences not from the reference. Thank you

for kraken2 output : ktImportTaxonomy -s 1 -m 2 -t 5 ngs.report -o krona.html

Here are the gbk files : [file1](https://drive.google.com/file/d/1ENFdjUMk2BJmQjKNApUQBg1l99FCvvep/view?usp=sharing) and [file2]( https://drive.google.com/file/d/1JC_IMlJf208DrfZWOBvjIGiomuAv3Guh/view?usp=sharing)

Thanks @hyphaltip @nextgenusfs it seems to work, but at the end i got that: funannotate annotate --genbank /sanhome2/data/FOA/Compare/gbk/Fusarium_oxysporum_f.sp._albedinis.gbk --cpus 56 -o test1 ------------------------------------------------------- [Aug 23 11:13 AM]: OS: Ubuntu 14.04,...