BBMap/BBTools reformat.sh : real error or spurious message? [W::bgzf_read_block] EOF marker is absent reformat.sh

Question

[ilya_shl]

When subsampling paired-end .fastq.gz files using reformat.sh from BBMap/BBTools, I get this error message:

[W::bgzf_read_block] EOF marker is absent reformat.sh

I've checked the input files with gunzip -t, no error. The input files are a concatenation of bcl2fastq outputs from two lanes. reformat.sh seems to complete with no error code, but is this error message safe to ignore? Similar report in another post.

Thanks for help!

Answer 1

[GenoMax]

@Brian Bushnell (author of BBTools) had said this a while back when I asked him about this message:

It seems to be a bug in bgzip (which I'm using now as the default compressor because it's much faster than pigz and can decompress multithreaded), or just overly cautious verbose messaging. You can add the flags "bgzip=f unbgzip=f" to make it not use bgzip, in which case it will revert to pigz, and the message will go away. I verified that for files where the message occurs, the output is identical when decompressed with bgzip, pigz, and Java's internal gzip decompressor.

So you can either ignore the message or use the options mentioned above.