ERROR: Read name line should start with '@'

[qquuzhao]

ERROR: Read name line should start with '@'，I used fastp 0.23.3 to deal my data. But when I use fastp.0.23.0,it's not occured this ERROR。I think this version is missing to handling of these abnormal reads.Looking forward to your response.

[sfchen]

Can you upload the data that failed?

[erinyoung]

I am so glad that someone else ran into this problem!

I have some examples because I'm running into the same issue with some paired-end SARS-CoV-2 files that I use for a lot of my testing.

They are located at:
https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz
https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123_2.fastq.gz

[nh13]

s10.R1.fq.gz
s10.R2.fq.gz

fastp \
        --in1 s10.R1.fq.gz \
        --in2 s10.R2.fq.gz \
        --out1 s10_1.fastp.fastq.gz \
        --out2 s10_2.fastp.fastq.gz \
        --json s10.fastp.json \
        --html s10.fastp.html \
         \
         \
         \
        --thread 2 \
        --detect_adapter_for_pe

fastp --version
fastp 0.23.3

The smoking gun is this:

$ file s10.R1.fq.gz
s10.R1.fq.gz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 8883

When I decompress and recompress with gzip, it runs just fine (similarly with decompressed FASTQ).

I also decompressed and recompressed with bgzip, and it fails.

[zerobio]

I also encountered this problem. I guess whether the differences as shown out result in the error ?

[sfchen]

@zerobio rooted it as you pointed.

I will fix and update it soon.

[sfchen]

Please try v0.23.4

[shenwei356]

Binary at http://opengene.org/fastp/fastp is not updated yet.

[sfchen]

Yes, that will be updated tomorrow.

[sfchen]

Pre-built binary was just updated. But the conda version is still waiting for auto bump-up.

[matthdsm]

Can confirm this issue is fixed in the latest version!

[qquuzhao]

Thank you very much！Yes，the issue isfixed.

[nh13]

Confirms it works on bgzip'ed FASTQs posted above, thank-you!