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BigelowLab / edna-dada2

Maine eDNA dada2
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incomplete preprocess run for PacBio 18S sequences #33

Closed abooker10 closed 9 months ago

abooker10 commented 1 year ago

Hi dada2 team-

I am running into an issue getting the preprocessing step to work for pacbio 18s data. I am following the instructions here: https://github.com/BigelowLab/edna-dada2/wiki/Processing-PacBio-reads

I think my preprocess run was a partial success because a filter_and_trim.csv was generated, but I did not get a truncLen.csv which is required for the post processing step.

I am attaching all my files because I am not sure what direction to go in to remedy this. job_submission.sh job_submission.sh.txt

the preprocess yaml file - I had to edit the filtering min and max in this file to accommodate my samples pacbio_preprocess.yaml.txt

the preprocess R file pacbio_preprocess.R.txt

the post process yaml - I did not edit this file pacbio_postprocess.yaml.txt

the error and output files from the run run_dada2_pipeline.o2671568.txt run_dada2_pipeline.e2671568.txt

the Log file from the preprocess run log.txt

the audit file from the preprocess run audit.txt

Thanks for any advice on how to get the truncLen.csv file generated during the preprocess run.

Sincerely, Anne

robinsleith commented 1 year ago

Hi Anne, I think the truncLen might be carryover from the illumina workflow. I just checked and my pacbio test did not create truncLen but the postprocess worked fine. What happens if you just run it?

abooker10 commented 1 year ago

Hi Robin- It worked without the truncLen file! Thank you, and apologies I did not try that on my own. Anne

btupper commented 9 months ago

@robinsleith @abooker10 Can we close this?

abooker10 commented 9 months ago

In my understanding we can, thanks for all the help!

Anne

On Thu, Jan 25, 2024 at 2:39 PM Ben Tupper @.***> wrote:

@robinsleith https://github.com/robinsleith @abooker10 https://github.com/abooker10 Can we close this?

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