[W::bgzf_read_block] EOF marker is absent in BBMAP
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3 months ago
Nunu ▴ 10


I'm asking an issue encountered in bbmap. I was using bbmap to remove host contaminants from my microbiome data. The commands are simple as below (ref folder already generated in the last step)

bbmap.sh -Xmx42g in=R1.fastq.gz in2=R2.fastq.gz outu=cleaned.interleaved.fastq.gz threads=12 overwrite=t unpigz=t usejni=t bbmap.log

It went through all fine and the output was generated as well. However, when I check the log file, I noticed [W::bgzf_read_block] EOF marker is absent. The input is probably truncated. Can anyone tell me if this is something that I need to concern?

Started read stream.
Started 12 mapping threads.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11

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