manifest file issue while doing 16s rna for small read in qiime2

General Discussion
1

hi everyone ,

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /home/anjali/bioinfo2/short_read/Data1_16S_SRA/manifest.tsv --output-path paired-end-demux.qza --input-format PairedEndFastqManifestPhred33V2
There was a problem importing /home/anjali/bioinfo2/short_read/Data1_16S_SRA/manifest.tsv:

/home/anjali/bioinfo2/short_read/Data1_16S_SRA/manifest.tsv is not a(n) PairedEndFastqManifestPhred33V2 file:

There was an issue with loading the metadata file:

Metadata IDs must be unique. The following IDs are duplicated: 'SRR34626484'

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: Metadata in QIIME 2 — QIIME 2 2024.10.1 documentation

2

Hi @Anjali_20, Welcome to the QIIME 2 Forum. The error message you shared describes the most likely cause of the issue:

It seems that one of your sample ids is showing up multiple times. If you address this, you should be good to go. If you need help created manifest files, you can try out this experimental tool.

5

@Anjali_20, another moderator suggested that since these look like SRA IDs, using q2-fondue to directly download from SRA into QIIME 2 artifacts might make this easier for you. See this post. q2-fondue is now installed as part of QIIME 2 (amplicon) and MOSHPIT (metagenome), so as long as you've installed a recent version of either you should be ready to use it.

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6

thankyou for the solutions

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