I tried to import compressed fastq files (two files each sample with one forward and one reverse file) using the command shown below with qiime2-2018.6 in Miniconda3 environment.
qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path QIIME --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza
I could not import the files because of the following error messages.
There was a problem importing /QIIME:
Unrecognized file (/QIIME/miniconda3/pkgs/ncurses-5.9-10/share/terminfo/61/att5420-w-rv-n) for CasavaOneEightSingleLanePerSampleDirFmt.
I appreciate if you can guide me on how to fix this problem.
Try to import your fastq following ‘fastq manifest’ format. You can find the details in Importing data tutorials
Thanks Shaan for you reply!
I have over 1000 paired-end demultiplexed fastq files. Can ‘fastq manifest’ format be used for importing for my files? If it is ok, which one I should use, PairedEndFastqManifestPhred33 or PairedEndFastqManifestPhred64?
That depends on the sequencing technology. If your data is relatively new, than it is almost certainly Phred33, but you should check with your sequencing center to verify.
The 33/64 part refers to how the Phred quality scores are encoded in the fastq file. Without knowing the offset (33 or 64) we can’t actually know the real quality scores.
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