Comments (5)
Hi @ospfsg,
the error states that the config file is not valid, so the minimal edits seem to have broken something. Check that you do not mix tabs and spaces, for instance, and that everything is indented as in the original file.
Can you post the file here, so that I can have a look?
Cheers
Lucas
from grenepipe.
Also, in reply to your emails, I'll answer here, as this might be interesting for others as well:
The --conda-prefix
option:
As far as I understand, is just a folder (always the same) where to where snakemake download the environments, but not relevant or useful for the analysis...
Yes, this directory can be specified to avoid re-downloading all the packages from conda every time you run the pipeline. By using the same directory for every analysis that you run, you will save time. Other than that, it does not change the analysis.
I find the pipeline very useful and if it works I as expect I would like to ask to be installed in the Portuguese Network of advanced Computing (https://rnca.fccn.pt/)
Thank you, happy to hear! As for installing: The things that need to be installed are conda and Snakemake, as described in the grenepipe wiki. Then, grenepipe itself just needs to be downloaded to somewhere to be used, but no installation step per-se is necessary.
for instance for fastp I am using this extra params below. Is this the correct syntax?
# ---------------------------------------------------------------------- # fastp # ---------------------------------------------------------------------- # Used only if settings:trimming-tool == fastp # See fastp manual: https://github.com/OpenGene/fastp fastp: threads: 100 # Extra parameters for single reads. se: "" # Extra parameters for paired end reads. pe: "-g -l 80 -p -q 20"
It generally looks correct, but your email has messed up the indentation of the first line. Not sure if that is in your file as well. YAML is sensitive to that (similar to Python), and so the indentation needs to be kept as-is, and no tabs and spaces can be mixed.
I hope I replied to all your questions from the emails. If not, please let me know here :-)
Cheers
Lucas
from grenepipe.
Hi @ospfsg,
in reply to your email:
Dear Lucas
I build a new config.yaml file. I attached it. Again minimal editing.
the same results:
(grenepipe) dau1@frey:~/software/grenepipe-0.12.2$ snakemake -nq --use-conda --conda-frontend mamba --> cores 60 --directory /mnt/data1/Project_KeePace/Operational/4_data_analysis/5_grenepipe/run1/ --conda-> prefix /home/dau1/software/conda-envs/ WorkflowError in line 28 of /home/dau1/software/grenepipe-0.12.2/rules/common.smk: Config file is not valid JSON or YAML. In case of YAML, make sure to not mix whitespace and tab > indentation. File "/home/dau1/software/grenepipe-0.12.2/Snakefile", line 7, in <module> File "/home/dau1/software/grenepipe-0.12.2/rules/common.smk", line 28, in <module>
The config file is in RUN1 directory
snakemake is run from the grenepipe directory
Best
osp
with this attached config file: config.zip
The issue is that on line 7, you added some path to a directory:
data: "/mnt/data1/Project_KeePace/Operational/1_raw_data/"
which is not meant to be there. Only edit numbers, texts, and paths where the original file has them, otherwise you'll get an error. The data:
line in the yaml file is the start of the group of options related to data, similar to the settings:
on line 46. It is not meant to have any string following.
I assume that the directory that you are giving there is where your fastq files are? The locations of those files are specified in the samples table instead - no need to add any directory path for them.
Hope that helps
Lucas
from grenepipe.
PS: You can also try tools such as https://www.yamllint.com/ to verify your file beforehand :-) In your case, it fails to give the exact cause of the error, but at least tells you whether the file is valid.
from grenepipe.
Hi @ospfsg,
from your recent email, I understand that you got it work now, great! I'm going to close this issue then. For any further questions and problems, simply open a new one then. GitHub Issues are the preferred way for questions, rather than email.
Thank you and so long
Lucas
from grenepipe.
Related Issues (20)
- MissingRuleException HOT 13
- PID error HOT 9
- java.lang.OutOfMemoryError: Java heap space HOT 2
- GRENEPIPE v12.1 HOT 5
- Make "trimming-tool" optional HOT 4
- restrict-regions and short contigs HOT 2
- ModuleNotFoundError: No module named 'chardet' HOT 2
- Write full executed command for each step to log files for reproducibility HOT 3
- merging calls from multiple pipeline runs? HOT 2
- mamba is difficult to install in grenepipe environment HOT 6
- Feature Request: Download reference genome and known variation HOT 2
- greenepipe run error HOT 5
- problem with dedup HOT 4
- a new type of error HOT 2
- a new type of error HOT 1
- another type of error HOT 11
- permission denied error HOT 5
- not sure what the issue is HOT 11
- --rerun-incomplete flag repeat mapping step for all samples HOT 4
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