Probblems with Manifest import

I am trying to import my manifest file with the following command:

qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path manifest.csv --output-path paired-end-demux_seqs.qza --input-format PairedEndFastqManifestPhred33

I am getting the following output error:

There was a problem importing manifest.csv:

/tmp/q2-SingleLanePerSamplePairedEndFastqDirFmt-4g7rkxch/pH-9_5%NaCl_9_L001_R2_001.fastq.gz is not a(n) FastqGzFormat file:

Header on line 5 is not FASTQ, records may be misaligned

Would you please help me solving itmanifest.csv (1.6 KB) S16-16S_V3-V4_C5R52_TGCAGCTA-GCGTAAGA_L001_R2.fna.gz (4.2 MB)

Good morning, Sakshi,

Thanks for posting your files, especially your .fna.gz file.

So the error says

.fastq.gz is not a(n) FastqGzFormat file

Which makes sense, because the file you posted is a .fna.gz file, (so fasta not fastq). If you list your fastq files (instead of fasta), this should solve the problem.

Let me know if this works well for you,


Thank you Colin. It worked.

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.