search

marbl / VALET

A pipeline for detecting mis-assemblies in metagenomic assemblies.
MIT License
14 stars 4 forks source link

SyntaxError: invalid syntax #11

Open blancaverag opened 4 years ago

blancaverag commented 4 years ago

After installing the program according to instructions provided here I try a run with the test data and get the following error: 

src/py/valet.py --skip-reapr -a test/c_rudii_reference.fna,test/c_rudii_dup.fna,test/c_rudii_relocation.fna,test/c_rudii_reloc_dup.fna -1 test/lib1.1.fastq -2 test/lib1.2.fastq --assembly-names reference,duplication,relocation,reloc-dup
  File "src/py/valet.py", line 854
    with open(bin_path + '/reapr/03.score.errors.gff', 'r') as reapr_gff, \
                                                                        ^
SyntaxError: invalid syntax

I am not sure why it is related to reapr, if I added "--skip-reapr" (I am not able to install REAPR in my machine).

Would you have any idea of the problem here?

Thank you in advance