itsxpress plugin

Hello, the error I am receiving is this:
Plugin error from itsxpress:
1C515_10_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:
Missing sequence for record beginning on line 5.
This is what I’ve done:
qiime itsxpress trim-pair-output-unmerged --i-per-sample-sequences ITS_1A_raw_alice.qza --p-region ITS2 --p-taxa F --p-cluster-id 0.97 --p-threads 3 --o-trimmed trimmed_ITS_alice.qza

Hi @Alice_Calvo,
welcome in the forum!

It seems there is a problem in the R1 file for sample 1C515, some sequence seems missing!
Can you open it and look at the first few lines?

Hi thanks for all. I’ve checked the file and it seems to be ok. Now I’m trying to do everything again from the beginning. (qiime2-2021.2) [email protected]:~/Desktop/Urban_Jungle/prova$ qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-format PairedEndFastqManifestPhred33 --input-path manifestITSalice.txt --output-path ITS_1A_raw_alice.qza
Imported manifestITSalice.txt as PairedEndFastqManifestPhred33 to ITS_1A_raw_alice.qza
(qiime2-2021.2) [email protected]:~/Desktop/Urban_Jungle/prova$ qiime itsxpress trim-pair-output-unmerged --i-per-sample-sequences ITS_1A_raw_alice.qza --p-region ITS2 --p-taxa F --p-threads 3 --o-trimmed 1A_ITS_trimmed_alice.qza
Maybe there was a problem in the first file ITS_1A_raw_alice.qza, anyway now I’m waiting to see if it’s all ok.
Thank you very much

Hi @Alice_Calvo,

Another test you could do in meantime it to try to process the ‘ITS_1A_raw_alice.qza’ artifact with a different plug in, to see if it may give a different error/information on your file, eg trimming a primer sequences with cutadapt or try merging the sequences with vsearch.

Keep us posted