Importing fastaq for qiime2

Hi there!
I am new for qiime2. I am trying to import my Illumina data. The company sent me two types of files for each treatment: forward and reverse fastaq.gz and merged file, also fastaq.gz. According to the company, demultiplexing has already been done.
The “look” of forward file is:

I have prepared a manifest with sample-id, forward-absolute-path, reserve-absolute-path, and followed the tutorial example:

qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path /Users/claudiavic/DS4
–output-path reads.qza \

Am I selecting the wrong type of data? Please help!

Regards, CV

Hi @CVicent,

You need to add the --input-format flag, in your case, I think i t should be --input-format PairedEndFastqManifestPhred33V2.

So, your new, full comamnd will be

qiime tools import
--type ‘SampleData[PairedEndSequencesWithQuality]’
--input-format PairedEndFastqManifestPhred33V2
--input-path /Users/claudiavic/DS4
--output-path reads.qza \


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Hi @jwdebelius,

thank you for your prompt answer. I have made changed the command as you indicated. But now I have another error.

My manifest is:

I cannot understand why I have “t” in the table headers. I have prepared the file on BBEdit.

Could you help me with this? I cannot run keemei since I’m Mac.

Regards, CV


From what I recall, your column title should be: “forward-absolute-filepath” and there should be another column for “reserse-absolute-filepath” in your manifest.

Also I can see your R1 and R2 files are in the same column, it is likely the R2 file is a reverse sequencing file and should be in the revervse column. Ben

edit: Your sampleid should likely be MS1, MS2 and so on --> the MS1_R1 and MS1_R2 likely reflects the forward (R1) and reverse (R2).

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@jwdebelius and @ben,
I got the error. I had hidden letter in my manifest file, and prepared again according to @ben suggestions. I saw the green letter :star_struck:

Thank you both. Best CV


Green letters are the best. Ben

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