DRL/blobtools

blobtools create tool error

XClaws opened this issue · 3 comments

XClaws commented

Dear team.
I have encountered a error during blobtools create for example, here is the error report.

python blobtools.py create
-i example/assembly.fna
-b example/mapping_1.bam
-t example/blast.out
-o example/my_first_blobplot
[+] Parsing FASTA - example/assembly.fna
[ERROR:28] : Please specify "--names" and "--nodes", or "--db"

lukesarre commented

I am experiencing this problem. Has anyone found a solution?

DRL commented

Hi,

maybe it's the wrong python executable.

And maybe better to run it as

./blobtools create
-i example/assembly.fna
-b example/mapping_1.bam
-t example/blast.out
-o example/my_first_blobplot

cheers,

dom

Deleted user commented

I had the same issue when downloading blobtools from the release page. In the release version the NCBI nodeDB is not included. So you need to do the steps provided in the documentation by yourself ("Download NCBI taxdump and create nodesdb"). This way a default database is created and can be used by the script.