import data in qiime 2

Hi. I am trying to import paired-end reads that demultiplexed into QIIME2. I uploaded my photo of my data file, manifest file, and version of conda and qiime and error. what is this error? I search in qiime 2 forum but I don't see anything about this error.

Hi @elaheahmadi,

Thanks for posting your commands and file names. Your problem looks similar to this post here.

You are missing the'source-format' parameter in your command and the default format of ‘SingleLaneSamplePairedEndFastqDirFmt’ is not right for your situation. Just override this by adding --source-format PairedEndFastqManifestPhred33 or --source-format PairedEndFastqManifestPhred64 depending on which format you have. This is described in the importing tutorial, at the bottom of the 'fastq-manifest-formats’ section.
Lastly, make sure that either your --input path gives the correct path to your manifest file, or that you are entering the script from the directory in which it is in. Let us know if you are still running into any problems. Good luck!

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thank you so much your quick response. i enter --source format PairedEndFastqManifestPhred64 and 33. show me different error that i see its similar in forum but i check my manifest and i dont see mistake. please help me.

Hi @elaheahmadi,
That’s good, that means we’re getting closer!
First thing I wanted to point out is that unless you know for a fact that your quality scores are phred64, it’s more likely they are phred33. 64 is based on the older systems. You can confirm this by asking your sequencing facility.
The new error you are getting now is basically telling us that the address you’ve given in your manifest file is not correct, or perhaps there is some sort of access issues which you might not have proper access rights. Let’s focus on the first possibility.
Your manifest file indicates that the addresses start at the working directory -> $PWD. The importing tutorial indicates that you should use absolute filepaths. Can you double check to make sure that your files are indeed inside/home/elahe/paired/ ? If not, you can locate your files and use their absolute paths instead in your manifest file.
If you still get an error once we confirm the appropriate location we can then troubleshoot further regarding access rights, but I think it’s probably a location issue.

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Dear Mehrbod
thank you so much. my problem resolved. result of this command
Saved Visualization to: demux.qzv
i apologize from you if i take your time.
if i have question again please help me.

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