Input problem-fastq.gz is not a(n) FastqGzFormat file, Invalid separator on line 58847

Hello everyone,
I am doing research about gut microbiota, I got the raw data and i was hoping to input them into qiime2, but there was always problems. I copied the code and output here.

(qiime2-2019.10) [email protected]:~$ qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path /home/pjj0702/chicken1/ftm1/ --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path /home/pjj0702/chicken1/reads_qza/demux.qza
There was a problem importing /home/pjj0702/chicken1/ftm1/:

/home/pjj0702/chicken1/ftm1/T9_S11_L001_R2_001.fastq.gz is not a(n) FastqGzFormat file:

Invalid separator on line 58847

Can anybody give me some instruction?
Thank you in advance!

Hi @Kimki_Pang!

Yes! You came to the right place...

The error message says "Invalid separator on line 58847", which means somewhere around line 58847 in the file T9_S11_L001_R2_001.fastq.gz your fastq appears to be corrupt, invalid, or malformed. Specifically, the error message is complaining about not finding a + sign (record separator) on line 58847). You can open the file open and review the file around line 58847 to learn more. I would also suggest you consult with whoever did the sequencing and/or file prep for you, just to make sure you know all of the pre-processing steps that were applied.

Thanks!

:qiime2:

1 Like

Hi Matthew, thank you for your answer, I finally figured out that I should decompress my data in a different way, otherwise the data tend to be missing some parts, which caused the problem I met.