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a-h-b / dadasnake

Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
GNU General Public License v3.0
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WorkflowError: File reporting/primerNumbers_perLibrary.tsv marked for report but does not exist. #33

Closed tboonf closed 1 year ago

tboonf commented 1 year ago

I have installed the program and have no issue in running the rest run. However, when i tried to run test dataset using config.16S.yaml, I was prompted with the error message as above. I have modified the config file in the section of raw and output directory, as well as the database for Silva. Complete error message is below:

Building DAG of jobs... Creating report... Missing metadata for file workflow.done. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning. Missing metadata for file primers.done. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning. Missing metadata for file preprocessing/2/sample_2.fwd.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning. WorkflowError: File reporting/primerNumbers_perLibrary.tsv marked for report but does not exist.

Please help.

a-h-b commented 1 year ago

Hi - thanks for reaching out. Can you let me know the command you used for starting this? Best wishes - AHB

tboonf commented 1 year ago

This is the command i used: ./dadasnake -n "TESTRUN2" -r config/config.16S.yaml

a-h-b commented 1 year ago

oh, yes only run reporting... you need to include -c or -f or -l to actually run the pipeline (see ./dadasnake -h).

tboonf commented 1 year ago

Thank you. Now that has been resolved. Very helpful. I have gone ahead and tried using my own data. All went well until i received this error message: Error in rule dada_dadaSingle_pool: jobid: 12 output: merged/dada_merged.RDS log: logs/DADA2_read2RDS.log (check log file(s) for error message)

When I checked the log file, this was what described: "Error in dada_uniques(names(drpi$uniques), unname(drpi$uniques), names(drpi$uniques) %in% : Rounded quality exceeded range of err lookup table."

Would appreciate any help to resolve this. Thank you :-)

a-h-b commented 1 year ago

Hi, okay, so that's a new error... what kind of data do you have? (as in, what kind of quality values do you expect?

tboonf commented 1 year ago

It’s nanopore data

a-h-b commented 1 year ago

oh, okay... it doesn't do that (except if you did a pre-processing like in here: 10.1093/gigascience/giy140) , sorry. Or you can ignore the quality values, but that may not be a good choice...