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ErnakovichLab / dada2_ernakovichlab

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Recurring Quality Plot Error #10

Closed hhollandmoritz closed 1 year ago

hhollandmoritz commented 1 year ago

@science-chump is getting a recurring error when running quality plots:

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'dirPath' in selecting a method for function 'qa': internal: buf != <newline>
Calls: plotQualityProfile ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

It appears from some other posts that this might be due to an issue of not explicitly loading library(Biostrings) before loading dada2.

However it could also be due to a validation issue with the fastq files.

hhollandmoritz commented 1 year ago

Tried running this with the same data that @science-chump used. Files appear to become corrupted during the copying step from the trimmed folder to the preprocessed_F folder. No idea why this is happening.

Solved the problem by using file.symlink() instead of file.copy, so that files in the preprocessed_F and preprocessed_R directories are symlinks to their counterparts in the trimmed directory.