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combogenomics / medusa

A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.
http://combo.dbe.unifi.it/medusa/
GNU General Public License v3.0
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Bio module import error #27

Closed jananiharan closed 5 years ago

jananiharan commented 5 years ago

Hello,

I get the following error when attempting to build scaffolds even when I have the latest version of Biopython installed:

.....

reading input file "/home/janani/NovelStreptomycesWGS.May18/new6T.draft.Apr18/6T.direct.assembly/ref.genomes/GCA_002192455.1_ASM219245v1_genomic.fna" of length 8144417

matching query-file "/home/janani/NovelStreptomycesWGS.May18/new6T.draft.Apr18/6T.direct.assembly/ref.genomes/GCA_002192455.1_ASM219245v1_genomic.fna"

against subject-file "6T_GCA_002192455.ntref"

COMPLETETIME /opt/anaconda2/opt/mummer-3.23/mummer 6T_GCA_002192455.ntref 10.45

SPACE /opt/anaconda2/opt/mummer-3.23/mummer 6T_GCA_002192455.ntref 16.41

4: FINISHING DATA done.

File "medusa_scripts/netcon_mummer.py", line 247, in G=initialize_graph(query_genome) File "medusa_scripts/netcon_mummer.py", line 154, in initialize_graph from Bio.SeqIO import parse ModuleNotFoundError: No module named 'Bio' Exception in thread "main" java.lang.RuntimeException: Error: Network construction failed. at Scaffolder.scaffolder(Unknown Source) at Scaffolder.runOnTerminal(Unknown Source) at Scaffolder.(Unknown Source) at Scaffolder.main(Unknown Source)

Any suggestions on how to fix this error? Thanks!

mgalardini commented 5 years ago

Hi,

I believe you do not have the biopython module installed: you can do that by typing python -m pip install biopython, or refer to the package's documentation for alternative solutions.

Hope this helps, Marco