Hello! There does seem to be a problem with my manifest file. I tried the absolute file path, though it did seem to be in the correct directory (at bottom). I altered the names of the raw files so that they don't have the S## designation, but otherwise I can't see a problem:
ManifestRun2.csv (1.2 KB)
qiime tools import \
> --type 'SampleData[PairedEndSequencesWithQuality]' \
> --input-path ManifestRun2.csv \
> --output-path paired-end-demux2.qza \
> --source-format PairedEndFastqManifestPhred33
There was a problem importing ManifestRun2.csv:
ManifestRun2.csv is not a(n) PairedEndFastqManifestPhred33 file
(qiime2-2018.6) Cybeles-MacBook-Pro:qiime2-skate3 cybelecollins$ qiime tools import \
> --type 'SampleData[PairedEndSequencesWithQuality]' \
> --input-path /Users/cybelecollins/qiime2-skate3/ManifestRun2.csv \
> --output-path paired-end-demux2.qza \
> --source-format PairedEndFastqManifestPhred33
There was a problem importing /Users/cybelecollins/qiime2-skate3/ManifestRun2.csv:
/Users/cybelecollins/qiime2-skate3/ManifestRun2.csv is not a(n) PairedEndFastqManifestPhred33 file
Hey there @Cybele_C !
Okay, I took a look at the attached file, and to quote @ebolyen :
Your file contains what is called a Byte Order Mark at the very beginning (it’s completely invisible and meant only for the computer to read). We typically expect files to be encoded as UTF-8 (you may have heard of ASCII, this is the same thing, just more universal). While UTF-8 is ok with a byte order mark it isn’t actually useful since there is no byte order in UTF-8 (vs something like UTF-16).
QIIME 2 shouldn’t have given you any trouble for having the BOM, so there’s definitely something wrong on our end. I’ll try and figure out where an issue will go.
In the meanwhile, here’s a file with the BOM stripped:
ManifestRun2.csv (1.2 KB)
I removed the BOM, and attached above. Give that a shot and let us know!
@ebolyen and I are planning on addressing this during the 2018.10 development cycle, so stay tuned!
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Hello! I tried my original manifest file in text edit after pressing the delete button at the beginning. This worked.
Programming is very mysterious, but becoming more intriguing - deep into Wikipedia right now. Thank you for the new information and the help. I appreciate it so much.
1 Like
system
(system)
Closed
October 19, 2018, 8:04am
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