itsxpress plugin

Community Plugin Support
1

Hello, the error I am receiving is this:
Plugin error from itsxpress:
tmp/q2CasavaOneEightSingleLanePerSampleDirFmt-b484enqn
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

2

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?
Cheers
Luca

3

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) alice@alice-VirtualBox:~/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) alice@alice-VirtualBox:~/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

4

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
Luca