ERROR fmlrc2] Invalid record while parsing long read file: ParseError { msg: "invalid gzip header", kind: Io, position: ErrorPosition { line: 0, id: None }, format: None }

HudsonAlpha / fmlrc2

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ERROR fmlrc2] Invalid record while parsing long read file: ParseError { msg: "invalid gzip header", kind: Io, position: ErrorPosition { line: 0, id: None }, format: None } #35

Closed ytt01 closed 4 months ago

ytt01 commented 4 months ago

Hello, While correcting Nanopore data, I encountered the following issue with some files.

I used gzip -t to check the fastq.gz files and found that some of the individual files were not damaged, while others indicated the presence of trailing garbage(gzip: S21D567.fastq.gz: decompression OK, trailing garbage ignored). Do you have any suggestions for resolving this situation?

holtjma commented 4 months ago

Sounds like one or more of your fastq files is corrupt / incomplete. This is not something fmlrc will be able to resolve. You will likely need to contact your data provider to figure out what happened to the files you have or somehow clean up the file yourself.

holtjma commented 4 months ago

Closing due to inactivity, feel free to open for further inquiries.