pb-cdunn
commented
8 years ago File "/users/jurban/software/localpy/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.eggThat does not seem to be the virtualenv that you refer to elsewhere:
falcon_kit.mains.run args: ['/gpfs_home/jurban/software/falcon/FALCON-integrate/fc_env/bin/fc_run.py', 'fc_run.cfg', 'logging.ini']Did you "activate" the virtualenv? Maybe you need to re-activate. You should not be picking up any Python packages from outside the virtualenv.
I found that installing pyparsing in a certain falcon dir seemed to result in bypassing this import error ...
You should activate your virtualenv before running pip install. (And you should not use pip install -t.
p.s. I am also having trouble running falcon 0.4.0 with simulated fasta files. After searching issues and figuring out the error, it seemed like the fasta name and fasta formatting mattered.
Yes, DAZZ_DB/fasta2DB is very particular about fasta headers. It's aimed at PacBio data, but I do use it on my own simulated reads. There is a fasta2fasta in 0.5.2 that can help. Basically, you need:
>name/wellnumber/number_number
GATTACA...Maybe the num_num part can be any string, but the wellnumber should be unique for each read. DBsplit without -a will exclude all reads of the same wellnumber except the longest one; otherwise, all reads are retained.
JohnUrban
Hi,
It goes without saying, thanks for the great tools.
I have PacBio data that I can assemble with Canu, but want to try with Falcon.
I followed this procedure for installing Falcon 0.4.0 successfully:
The protocol above finishes without any errors -- it gets through what seems to be a test run at the end. I can then successfully assemble an ecoli dataset by making the config file compatible for SLURM:
falcon.slurm.in (batch script)
fc_run.cfg
However, replacing 0.4.0 with either 0.5.0, 0.5.1, or 0.5.2 in that same install protocol results in an unsuccessful installation. e.g.:
gets up to what seems like a test and fails:
It is complaining that there is no pyparsing module…. the pyparsing module is certainly available in my general environment though.
When I try to assemble the ecoli data set as done above, it also gives this type of error. I found that installing pyparsing in a certain falcon dir seemed to result in bypassing this import error and throwing another error:
Any ideas on how to successfully install the most recent version(s) would be greatly appreciated. I would be happy to answer any clarifying questions that might help you help me. Again, thanks for the great tools and support.
best,
John
p.s. I am also having trouble running falcon 0.4.0 with simulated fasta files. After searching issues and figuring out the error, it seemed like the fasta name and fasta formatting mattered. Nonetheless, I still have not been able to get falcon to run on simulated data… any advice on how to format a fasta file would be greatly appreciated.