Open ibseq opened 3 years ago
Hello,
I see you made this question almost a year ago but I´m having a similar issue:
VPIPE_BASEDIR = /home/geninfo/msisco/V-pipe/workflow
ModuleNotFoundError in line 21 of /home/geninfo/msisco/V-pipe/workflow/rules/common.smk:
No module named 'snakemake.sourcecache'
File "/home/geninfo/msisco/V-pipe/workflow/Snakefile", line 12, in
How did you solved it?
Thanks
Carol
@carolinasisco: which version of Snakemake are you using? Upgrading to the latest one (v6.13.1) could already solve your issue.
Hi, thank you for your reply. The snakemake version that was downloaded (following V-pipe installation manual) was 3.13.3. How can I upgrade it inside my V-pipe conda environment?
Also I´m running a pipeline for SARS-CoV-2 but using a different reference than the one stated on V-pipe, besides the config and metainfo files, is there another scrip that will need to be modified?
Again, thank you for your help
Hi,
The snakemake version that was downloaded (following V-pipe installation manual) was 3.13.3
The wiki is saddly out-dated - it matches older version 1.x and 2.x of V-pipe - and is in the process of being deprecated. (We should add "Warning" boxes about that, but hadn't had time yet).
More up-to-date example of installation include:
How can I upgrade it inside my V-pipe conda environment?
Note:
First make sure that all the relevant channels are enabled, you need conda-forge and bioconda, with a higher priority for the former:
# set the channel precedence (lowest to highest)
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
# NOTE conda-forge *HAS TO* be higher than bioconda
install mamba as this is now the conda package manager prefered by recent snakemake:
conda install mamba
now try updating snakemake:
mamba update --no-pin snakemake
warning: the no-pin allows to install also newer version of python, which might be required by more recent versions of snakemake, but might accidentally break other older package that you might have installed too.
Also I´m running a pipeline for SARS-CoV-2 but using a different reference than the one stated on V-pipe, besides the config and metainfo files, is there another scrip that will need to be modified?
Also of interest, once you have installed it, check the README.md in the config about how to configure it, and the latest documentation of the configuration format in config/config.html file in your local download (saddly, doesn't work online yet).
Specifically for your use case, check the options that are listed in the sars-cov2.yaml virus configuration as an inspiration in what you might want to adapt to your case.
Hi,
I deleted the current install and re-installed it using the quick install script. However when running dry--run I get this error:
FileNotFoundError in line 279 of /home/geninfo/msisco/V-pipe/workflow/rules/comm
[Errno 2] No such file or directory: 'config/samples.tsv'
File "/home/geninfo/msisco/V-pipe/workflow/Snakefile", line 12, in
Note that the samples file has been created and is located inside the workflow directory, it just seem that is not able to create the samples.tsv by checking the samples directory.
It's subtle difference dur to the most recent recommanded behaviours for modern snakemake workflows (see here: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html) - current recommendations are to put the TSV files in the config/
directory.
If you're running a recent version of V-pipe (2.99.1 or master), out-of-the box V-pipe will follow these recommendations and look for the tsv file in config/samples.tsv
. (But will not find this directory in your case).
If you prefere the older location (samples.tsv
, without a directory), you can set it in the configuration file, in the section "input" -> property "_samplesfile".
See the section about the changes sine V-pipe 1.0/2.0 in the config's README.md.
Hi, I keep getting this error:
VPIPE_BASEDIR = /home/geninfo/msisco/V-pipe/workflow
No virus base configuration, using defaults
AttributeError in line 230 of /home/geninfo/msisco/V-pipe/workflow/rules/common.smk:
'NoneType' object has no attribute 'setdefault'
File "/home/geninfo/msisco/V-pipe/workflow/Snakefile", line 12, in
Any advice?
thanks
Hi, we have updated the config's readme section about the samples TSV to make more clear some problem that can arise if the read-length isn't correctly set.
@carolinasisco :
AttributeError in line 230 of /home/geninfo/msisco/V-pipe/workflow/rules/common.smk: 'NoneType' object has no attribute 'setdefault' …. File "/home/geninfo/msisco/miniconda3/lib/python3.9/site-packages/jsonschema/validators.py", line 253, in validate
It's a problem when trying to validate your configuration.
Something is broken in your config.yaml
file (but saddly, the way the validation works in Snakemake, it doesn't give very useful messages).
Usually, you'll get 'NoneType' when you have an empty entry.
Something like:
general:
virus_base_config:
# empty no value here
output:
snv: true
…
in this example, section general property _virus_baseconfig will be a NoneType as there is no value assigned to it. (as opposed to output which is a section - it contains multiple properties - or svn - which is a Boolean: true/false).
Usually, you'll get 'NoneType' when you have an empty entry
Is there a way to fix it? I really need to use this program
Thank you for all your help
I really need to use this program
I know we're on different timezones, but you could quick drop on the chat at: https://gitter.im/V-pipe/community And we could quickly organise, e.g.: a Zoom meeting so you can show me what's exactly on your side.
Hi all, I run the above with own data but got : (vpipe_env) ibseq:~/testing/work$ ./vpipe --dryrun VPIPE_BASEDIR = /univ/ibseq/testing/V-pipe AssertionError in line 68 of /univ/ibseq/testing/V-pipe/rules/common.smk: ERROR: Line '13' does not contain at least two entries! File "/univ/ibseq/testing/V-pipe/vpipe.snake", line 11, in
File "/univ/ibseq/testing/V-pipe/rules/common.smk", line 68, in
from https://cbg-ethz.github.io/V-pipe/tutorial/sars-cov2/ any advice? thanks ibseq