According to this tutorial, the --input-path should be the folder holding your fastq files. Other --input-formats will use a manifest file, but not --input-format CasavaOneEightSingleLanePerSampleDirFmt.
Let me know if that works for you and keep on following those tutorials!
Thank you for your kind answer. I replaced the manifest file with the folder holding my fastq, and the program run successfully.
I am a bit confused at this point; how does Qiime2 know which file to use as manifest? Does it check all the text files in the working directory?
Nope. Qiime 2 only cares about the files you pass as input, and the location of the output.
I think the confusion is coming from all the different --input-formats that Qiime supports, and how it handles them differently. Take these two formats as examples:
--input-format CasavaOneEightSingleLanePerSampleDirFmt
This format opens up the --input-pathfolder, then it looks for fastq files inside that folder and makes one sample for each fastq file.
--input-format SingleEndFastqManifestPhred33
This format opens up the --input-pathfile, then it looks for fastq files listed in that file and makes one sample for each fastq file.
Does that make sense?
Colin
According to the documentation:
The manifest file is a comma-separated (i.e., .csv ) text file.
…So why don’t the examples on the website end with .csv? Looks like I missed that discussion. @thermokarst@mortonjt
Extensions are just a convention, you could have a comma-separated-values file that was called my-data.colinbrislawn and it would still technically be a CSV!
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thermokarst
(Matthew Ryan Dillon)
unassigned thermokarst
#8