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questions about qiime2 manifest file; error message: semantic type SampleData[SequenceWithQuality] does not have a compatible directory format.

I downloaded a fastq file from ENA and tried to make an artifact file (qza file) out of it using Qiime2.

the fastq file is a metagenome sample that is consisted of only one fastq file per sample, which I thought should be the forward sequence formed by Single-end-sequencing.

my manifest file looks like below

sample-id /home/ys_qiime_practice/ena_files

sample.1 /ena_files_3/SRR5202831/SRR5202831.fastq.gz

sample.2

and the code I used is from the Qiime2 tutorial, as below

qiime tools import \ --type 'SampleData[SequencesWithQuality]' \

--input-path se-33-manifest \

--output-path single-end-demux.qza \

--input-format SingleEndFastqManifestPhred33V2

then i got the error message saying: Semantic type SampleData[SequenceWithQuality] does not have a compatible directory format.

can you please help me sort this problem? thank you !

qiime2 manifest file qiime metagenome fastq
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updated by antonioggsousa antonioggsousa • written by seok1213neo • seok1213neo

1 answer

Hi,

Ideally you should post questions related with QIIME2 in their forum, since they put their efforts to provide feedback on QIIME2 users under their platform at: https://forum.qiime2.org/

Although I think the problem is your manifest file. You shouldn't change the header of the table and you should provide absolute file-paths as stated in the docs: https://docs.qiime2.org/2020.8/tutorials/importing/

sample-id   absolute-filepath
sample.1    /home/ys_qiime_practice/ena_files/ena_files_3/SRR5202831/SRR5202831.fastq.gz

Your sample.2 is empty, so I don't know what it is. As you see the header is not to be changed sample-id absolute-filepath. I think the table is tab-separated and not space.

I hope this helps to solve the issue.

António

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written by antonioggsousa antonioggsousa

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