avancise
commented
1 year ago Hey Nastassia,
Nice job getting to this point, that's awesome! The requirements for the html report are fairly specific to the MURI Mod 3 naming conventions and sample sheet, you're right. I think your two options from this point are:
1) adjust your sample sheet and sample names to match the format used by Mod 3 - if you want to go this route and are having trouble matching these formats, we can have a chat about how to do that. As long as you're using the fields in the sample naming conventions https://github.com/MMARINeDNA/metabarcoding_QAQC_pipeline/wiki/Preparing-Your-Data#sample-naming-conventions section the wiki, with no extra field or fewer fields, you should be good. It looks like you're using "MFU-FISH" as the primer name, which won't match our metadata sheets that call MiFish "MFU", so you'll likely need to adjust that to "MFU" 2) download the .Rmd file that makes the html report and adjust the code there to fit the format of your sample names and sample sheet. That might require a bit more up front work on your part right now, but down the line would likely require less adjustment of sample names and sample sheets.
Cheers, Amy
<)))>< <)))>< <)))>< <)))>< <)))>< <)))>< <)))>< <)))>< Amy M. Van Cise, Ph.D. (she/her/hers)
Assistant Professor Whale and Dolphin Ecology Lab http://amyvancise.com University of Washington | School of Aquatic and Fisheries Sciences 1122 NE Boat St, Box 355020 Seattle, WA 98105 Office: SAFS 216B 206-221-6118
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On Wed, Oct 11, 2023 at 6:08 PM Nastassia Patin @.***> wrote:
Hi team! I think I'm at a point where I can start posting issues here rather than individually emailing people, particularly because I think some problems will be widespread once others try to use the pipeline.
Although my "final_data" folder contains all the output files described in the wiki, the "analysis_output" folder is always empty. The wiki says for the preliminary analysis: "This is a quarto file that will take in the output files from DADA2 and create plots and statistics regarding read retention, read lengths, quality, and more." I think this is supposed to be an HTML output? In any case it would be great to get that final step working.
I think two issues might be preventing the preliminary analysis: 1) read file names that are different from the required format and 2) a metadata sheet that is different from the required format.
1.
Although I always try to rename the fastq files according to the formula, it's possible something is off. Here is an example of a read pair that I've renamed: MFU-FISH_001-d1-1_S1_L001_R1_001.fastq.gz and MFU-FISH_001-d1-1_S1_L001_R2_001.fastq.gz. Simplifying the requirements for raw read file names would be a huge help; I'm always nervous about renaming any raw data. 2.
The sample sheets we get from our sequencing center are quite different from the example sheet for the pipeline. I've uploaded an example raw file ("SampleSheet.csv") as well as a modified sheet that I made manually to try to match the example sheet ("SampleSheetUsed.csv"). In the long run, this is a big pain in the butt! Maybe we can simplify the metadata sheet requirements? I suspect something about the sample sheet is preventing the preliminary analysis but I'm not sure. In the last step of the pipeline I get an error that says "Run name not found." SampleSheet.csv https://github.com/MMARINeDNA/metabarcoding_QAQC_pipeline/files/12875927/SampleSheet.csv SampleSheetUsed.csv https://github.com/MMARINeDNA/metabarcoding_QAQC_pipeline/files/12875930/SampleSheetUsed.csv
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nvpatin
Hi team! I think I'm at a point where I can start posting issues here rather than individually emailing people, particularly because I think some problems will be widespread once others try to use the pipeline.
Although my "final_data" folder contains all the output files described in the wiki, the "analysis_output" folder is always empty. The wiki says for the preliminary analysis: "This is a quarto file that will take in the output files from DADA2 and create plots and statistics regarding read retention, read lengths, quality, and more." I think this is supposed to be an HTML output? In any case it would be great to get that final step working.
I think two issues might be preventing the preliminary analysis: 1) read file names that are different from the required format and 2) a metadata sheet that is different from the required format.
1) Although I always try to rename the fastq files according to the formula, it's possible something is off. Here is an example of a read pair that I've renamed: MFU-FISH_001-d1-1_S1_L001_R1_001.fastq.gz and MFU-FISH_001-d1-1_S1_L001_R2_001.fastq.gz. Simplifying the requirements for raw read file names would be a huge help; I'm always nervous about renaming any raw data.
2) The sample sheets we get from our sequencing center are quite different from the example sheet for the pipeline. I've uploaded an example raw file ("SampleSheet.csv") as well as a modified sheet that I made manually to try to match the example sheet ("SampleSheetUsed.csv"). In the long run, this is a big pain in the butt! Maybe we can simplify the metadata sheet requirements? I suspect something about the sample sheet is preventing the preliminary analysis but I'm not sure. In the last step of the pipeline I get an error that says "Run name not found." SampleSheet.csv SampleSheetUsed.csv