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DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
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blobtools create tool error #92

Closed XClaws closed 4 years ago

XClaws commented 4 years ago

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 3 years ago

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

DRL commented 3 years ago

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

ghost commented 3 years ago

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.