Incomplete deflate data

[xujiaweiouc]

Hi, When I finished " gunzip -c All_ONT.fastq.gz | NanoFilt -l 3000 | gzip > Clean.NanoFilt.fastq.gz", I want to see how many reads it has. So I ran ""pigz -dc Clean.NanoFilt.fastq.gz | awk 'NR%4==2{c++} END{print c}', but there are some errors for me. "pigz: skipping: Ath_clean.NanoFilt.fastq.gz: corrupted -- incomplete deflate data pigz: abort: internal threads error" So,what is the matter? Have a great day further and all the best. Kind Regards, Jiawei Xu

[wdecoster]

The file in your error message (Ath_clean.NanoFilt.fastq.gz) doesn't match the one in the command you mention (Clean.NanoFilt.fastq.gz). Are you sure you are using pigz on the right file? Based on the error it seems the .gz file was corrupted, possibly your NanoFilt command was interrupted?