Open husamia opened 2 years ago
creisle
commented
2 years ago @husamia Could you post the contents of the log file for the job that failed?
log: output_dir_full/logs/L1522785992-normal.validate.snakemake.batch-39.log.txt (check log file(s) for error message)
Built the docker image using Docker file provided with no errors.
You should not need to build anything. To use the mavis docker image with snakemake you will need to use singularity flag --use-singularity
husamia
commented
2 years ago cat output_dir_full/logs/L1522785992-normal.validate.snakemake.batch-39.log.txt
`2022-05-26 21:00:07,691 [INFO] MAVIS: 3.0.0
2022-05-26 21:00:07,692 [INFO] hostname: 7aa05bbe492b
2022-05-26 21:00:07,692 [INFO] arguments
2022-05-26 21:00:07,692 [INFO] command= 'validate'
2022-05-26 21:00:07,692 [INFO] config= '/app/mavis/output_dir_full/config.json'
2022-05-26 21:00:07,692 [INFO] inputs = ['output_dir_full/L1522785992-normal/cluster/batch-39.tab']
2022-05-26 21:00:07,692 [INFO] library= 'L1522785992-normal'
2022-05-26 21:00:07,692 [INFO] log= None
2022-05-26 21:00:07,692 [INFO] log_level= 'INFO'
2022-05-26 21:00:07,692 [INFO] output= 'output_dir_full/L1522785992-normal/validate/batch-39'
2022-05-26 21:00:07,722 [INFO] creating output directory: 'output_dir_full/L1522785992-normal/validate/batch-39'
2022-05-26 21:00:07,723 [INFO] loading: ['/app/mavis/reference_inputs/hg19.fa']
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/mavis/annotate/file_io.py", line 422, in load
self.content = self.loader(*self.name, **self.opt)
File "/usr/local/lib/python3.7/site-packages/mavis/annotate/file_io.py", line 256, in load_reference_genome
for chrom, seq in SeqIO.to_dict(SeqIO.parse(fh, 'fasta')).items():
File "/usr/local/lib/python3.7/site-packages/Bio/SeqIO/__init__.py", line 789, in to_dict
raise ValueError("Duplicate key '%s'" % key)
ValueError: Duplicate key 'chr1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/bin/mavis", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.7/site-packages/mavis/main.py", line 295, in main
raise err
File "/usr/local/lib/python3.7/site-packages/mavis/main.py", line 237, in main
library=args.library,
File "/usr/local/lib/python3.7/site-packages/mavis/validate/main.py", line 54, in main
reference_genome = ReferenceFile.load_from_config(config, 'reference_genome', eager_load=True)
File "/usr/local/lib/python3.7/site-packages/mavis/annotate/file_io.py", line 431, in load_from_config
return ReferenceFile(file_type, *config.get(f'reference.{file_type}', []), **kwargs)
File "/usr/local/lib/python3.7/site-packages/mavis/annotate/file_io.py", line 384, in __init__
self.load()
File "/usr/local/lib/python3.7/site-packages/mavis/annotate/file_io.py", line 426, in load
raise err.__class__(message)
ValueError: Error in loading files: /app/mavis/reference_inputs/hg19.fa. Duplicate key 'chr1'`
mattdoug604
commented
2 years ago Thanks for providing the logs @husamia. We'll try to look into this soon.
Describe the bug There is an error running the workflow as it is.
To Reproduce Built the docker image using Docker file provided with no errors. Downloaded the tutorial data and references needed per tutorial full. Then executed the tutorial workflow
root@7aa05bbe492b:/app/mavis# snakemake --jobs 1 --configfile=tests/full-tutorial.config.jsonExpected behavior I expected the results to be with no errors, however, I got error messages and the workflow didn't complete.
Input Data Tutorial data per documentation
Configuration Docker
Versions (please complete the following information):
Additional context I want to make sure I get the workflow running correctly with the tutorial data.