I am new QIIME2 user. I have fastq files in the form of paired end reads. I am using QIIME 2 via virtual box. I have downloaded the files and created a manifest file. I am now trying to convert these files to a qza so that i can start the trimming/cutadapt process.
I am using the following command, however i continue to get an error.
qiime tools import \
There was a problem importing manifest.txt:
/tmp/q2-SingleLanePerSamplePairedEndFastqDirFmt-x08c60m0/R5614_74_L001_R2_001.fastq.gz is not a(n) FastqGzFormat file:
Header on line 5 is not FASTQ, records may be misaligned
I would recommend checking the file format. Make sure the file is gzipped (I usually do this by first trying to open it and second trying to gunzip) and then check it. If the file has a problem, you will need to go back to the original source.