Open VerenaPass opened 7 months ago
sorry, I come late to this. I am starting to help bcbio community after joining the Harvard Chan Bioinformatics Core.
Can you let me know what MultiQC version you have installed now? I was wondering that you could try to downgrade the MultiQC version to the previous one. Did you find out how to skip multiqc?
Dear Laura, thanks for following up on this. I did not manage to skip multiqc unfortunately, I tried to turn it off but I still get the same error. MultiQC got installed together with bcbio 1.2.9 installation, but I cannot even check which version is installed because when I run multiqc --version I get:
Traceback (most recent call last): File "/home/passerini/resources/bcbio-1.2.9/anaconda/bin/multiqc", line 6, in <module> from multiqc.__main__ import run_multiqc File "/home/passerini/resources/bcbio-1.2.9/anaconda/lib/python3.7/site-packages/multiqc/__init__.py", line 16, in <module> from .multiqc import run File "/home/passerini/resources/bcbio-1.2.9/anaconda/lib/python3.7/site-packages/multiqc/multiqc.py", line 29, in <module> from .modules.base_module import ModuleNoSamplesFound File "/home/passerini/resources/bcbio-1.2.9/anaconda/lib/python3.7/site-packages/multiqc/modules/base_module.py", line 14, in <module> import markdown File "/home/passerini/resources/bcbio-1.2.9/anaconda/lib/python3.7/site-packages/markdown/__init__.py", line 42, in <module> from .core import Markdown, markdown, markdownFromFile File "/home/passerini/resources/bcbio-1.2.9/anaconda/lib/python3.7/site-packages/markdown/core.py", line 27, in <module> from . import util File "/home/passerini/resources/bcbio-1.2.9/anaconda/lib/python3.7/site-packages/markdown/util.py", line 32, in <module> from typing import TYPE_CHECKING, Generic, Iterator, NamedTuple, TypeVar, TypedDict, overload
Thanks! Verena
Hi,
I am using bcbio since a few years and it always worked nicely but last week after upgrading the tool I run a variant calling pipeline and got an error when running multiqc. I don't think it's the upgrade the problem but it might be that now multiqc requires python >= 3.8?!?
I paste below the error I got, but in the meantime I was wondering if I can run an alignment/variant calling pipeline skipping the multiqc step? I tried with tools_off: multiqc but it did not work.
Thanks,
Verena
Version info
bcbio_nextgen.py --version
): 1.2.9lsb_release -ds
): Scientific Linux 7.3 (Nitrogen)To Reproduce Exact bcbio command you have used:
Your yaml configuration file:
Log files (could be found in work/log) Log files are attached, here's the error:
bcbio-nextgen-commands.log bcbio-nextgen-debug.log