questions about qiime2 manifest file; error message: semantic type SampleData[SequenceWithQuality] does not have a compatible directory format.
1
0
Entering edit mode
13 months ago
seok1213neo ▴ 20

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 • 1.3k views
ADD COMMENT
0
Entering edit mode
13 months ago
antonioggsousa ★ 2.2k

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

ADD COMMENT

Login before adding your answer.

Traffic: 1786 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6