The bioBakery help forum

Preprocess Fail

Hi all,

I’m trying to get Metawibele to run on the demo data.
I installed using conda and have all the correct dependences (including the optional ones) but I am getting the following error

Traceback (most recent call last):
  File "/home/cwwalsh/miniconda3/envs/metawibele/bin/", line 179, in <module>
  File "/home/cwwalsh/miniconda3/envs/metawibele/bin/", line 152, in main
    assembly_dir, contigs)
  File "/home/cwwalsh/miniconda3/envs/metawibele/lib/python3.7/site-packages/metawibele/tools/", line 220, in assembly
    mylog = contig + ".log" 
NameError: name 'contig' is not defined

It looks as though it is looking for contigs have not been created (the Output/Preprocess/assembly directory is empty).

Any advice you have would be greatly appreciated.

P.S. the command I used to generate the error is below

metawibele preprocess \
           --input RawReads/ \
           --output Output/Preprocess/ \
           --output-basename demo \
           --extension-paired "_R1.fastq.gz,_R2.fastq.gz" \
           --extension ".fastq.gz" \
           --threads 4 \
           --config metawibele.cfg

Hi Calum,

Thanks for your interest in MetaWIBELE! This issue has been fixed in the new version of MetaWIBELE (v0.4.2). We have released it to pip and conda. And the Docker image will come out soon as well. Please feel free to try this new version.