jtoy7
commented
3 years ago So it looks like it was an issue with the python version. I downgraded from python 3.8 to 3.6 and it seems to have resolved the issue. However, now, when I try to run any dammit databases command, the program stalls out with a forever blinking cursor after printing:
dammit a tool for easy de novo transcriptome annotation by Camille Scott v1.2, 2018 submodule: databases
So close, but yet so far...any advice in getting this working is appreciated!
I just tried to install dammit on a cluster using conda. Per the bioconda site, I ran:
`conda create -n dammit python=3
source activate dammit
conda config --add channels conda-forge conda config --add channels bioconda
conda install dammit`
The installation seemed to run successfully, as there were no error messages. However, when I try running
dammit databasesor any other dammit command, I get the following errors:Traceback (most recent call last): File "/hb/groups/bernardi_lab/programs/miniconda3/envs/dammit/bin/dammit", line 5, in
from dammit import app
File "/hb/groups/bernardi_lab/programs/miniconda3/envs/dammit/lib/python3.8/site-packages/dammit/app.py", line 13, in
from dammit import annotate
File "/hb/groups/bernardi_lab/programs/miniconda3/envs/dammit/lib/python3.8/site-packages/dammit/annotate.py", line 13, in
from shmlast.app import CRBL
File "/hb/groups/bernardi_lab/programs/miniconda3/envs/dammit/lib/python3.8/site-packages/shmlast/app.py", line 3, in
from doit.tools import run_once, create_folder
File "/hb/groups/bernardi_lab/programs/miniconda3/envs/dammit/lib/python3.8/site-packages/doit/init.py", line 33, in
from doit.doit_cmd import get_var
File "/hb/groups/bernardi_lab/programs/miniconda3/envs/dammit/lib/python3.8/site-packages/doit/doit_cmd.py", line 15, in
from .cmd_run import Run
File "/hb/groups/bernardi_lab/programs/miniconda3/envs/dammit/lib/python3.8/site-packages/doit/cmd_run.py", line 9, in
from .runner import Runner, MRunner, MThreadRunner
File "/hb/groups/bernardi_lab/programs/miniconda3/envs/dammit/lib/python3.8/site-packages/doit/runner.py", line 8, in
import cloudpickle
File "/hb/software/apps/python/gnu-3.6.2/lib/python3.6/site-packages/cloudpickle/init.py", line 3, in
from cloudpickle.cloudpickle import *
File "/hb/software/apps/python/gnu-3.6.2/lib/python3.6/site-packages/cloudpickle/cloudpickle.py", line 151, in
_cell_set_template_code = _make_cell_set_template_code()
File "/hb/software/apps/python/gnu-3.6.2/lib/python3.6/site-packages/cloudpickle/cloudpickle.py", line 132, in _make_cell_set_template_code
return types.CodeType(
TypeError: an integer is required (got type bytes)
Other than seeing that a bunch of python scripts aren't functioning, I can't tell what's going wrong. Agian, it seemed to install just fine, so I feel like there must be some other issue? Has this happened to anyone else?