when I run the qiime tools import with the different parameters >>> qiime tools import --type EMPPairedEndSequences --input-path emp-paired-end-sequences --output-path emp-paired-end-sequences.qza<<<<
I have this error message >>>>> There was a problem importing emp-paired-end-sequences:
emp-paired-end-sequences/reverse.fastq.gz is not a(n) FastqGzFormat file:
File is uncompressed.
Can someone help me zith this issue.
Just like the error says, Qiime expects your files to be in the FastqGzFormat.
Can you post a few of the file names from the emp-paired-end-sequences directory?
Following up on @colinbrislawn’s suggestion here - it sounds like you might not have
gzipped your files, but rather renamed them to the extensions
.fastq.gz. How about you try something like this:
barcode-reads.fastq forward-reads.fastq reverse-reads.fastq
cp my-raw-seqs/barcode-reads.fastq emp-import/barcodes.fastq
cp my-raw-seqs/forward-reads.fastq emp-import/forward.fastq
cp my-raw-seqs/reverse-reads.fastq emp-import/reverse.fastq
You will need to update that a bit to match your file names, etc, but that should hopefully give you the general idea. If you get stuck, you know where to find us!
Hello @colinbrislawn and @thermokarst,
I was just following the ACATAMA-soils tutorial so I used the wget command to have the set of data provided in the tutorial, in the emp-paired-end-sequences directory i have three files : barcodes.fastq.gz forward.fastq.gz and reverse.fastq.gz.
At the end I have just removed the extention .gz and used the gzip command, now it works !!! a bit strange
Thank you for your response
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