First of all - Hello! I'm strongly new in b/i and qiime2 too, so, please dont throw your slippers!
It seems to me that I lost some important info about crossinteractions between --type and --input-format in deep caves of documents.
I'm trying to import some data from Index of /pub/databases/metagenomics/taxon_benchmarking to qiime2 (amplicon 2024.10 installed by conda) as any type of sample data. I found that it is training paired-end datasets, so I tried to import it via:
qiime tools import --input-path A100_V4_10K_1_human-gut.fastq.gz --input-format FastqGzFormat --type SampleData[JoinedSequencesWithQuality] --output-path A100.qza.
As I see there is no reason to use any of "PairedEnd" types coz I'm trying to import one file.
Error I'm catching sounds like:
No transformation from <class 'q2_types._util.FastqGzFormat'> to <class 'q2_types.per_sample_sequences._formats.SingleLanePerSampleSingleEndFastqDirFmt'>... phew, really long names.
I tried to solve it using different types and formats and got the same if changing types.
I can't figure it out. I searched for the problem and found similar, but posted solution is not actual for me.
Asking for help, thank you!
Hi @Nafan,
A quick question. Are you just trying to import one metagenomic fastq file like in your command or is this just an example?
either way, I think that the easiest way to import this is to create a manifest and import the file(s) that way. Here is a link to our docs on importing with a manifest!
https://docs.qiime2.org/2024.10/tutorials/importing/#fastq-manifest-formats
Yup, I wanna import just that one. May be Iām wrong with it, but as a result of lack experience I cant appreciate. Thank you for advice, will try!
Okay, found it, I lost another file with rev-reads. Sorry for alarm. Problem solved via two fq.gz and standard import, thank you again!)
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