installation issue on CentOS6.9 about fastp HOT 6 CLOSED

Your zlip is too old that it doesn't have functions like gzbuffer or gzoffset.

You can update the zlip, or just download the binary distribution from http://opengene.org/fastp/fastp , and run chmod a+x fastp to make it executable.

from fastp.

Alright, thanks for the quick reply.

Running fastp on a fastq.gz file of nanopore data throws an error, not sure why:

$ fastp -t 20 -i fail/fastq_runid_fff19c6dcf86112967c3df0777ebeddda1109a40_1.fastq.gz -q 8 -l 5000 -o out
Detecting adapter for single end input...
No adapter detected

terminate called after throwing an instance of 'std::system_error'
  what():  Enable multithreading to use std::thread: Operation not permitted
Aborted (core dumped)

Perhaps would be more appropriate in a separate thread, but do you think it would be possible to have fastp read from stdin and write to stdout?

from fastp.

Thanks for your information.

I compiled that binary on Ubuntu, and seems it is not working on centOS.

I recompiled one in CentOS, you can download it from: http://opengene.org/fastp/fastpcentos

And another option is to update your old zlib, then compile by your self.

from fastp.

And I also haven't tried any nanopore data, could you send me one or upload one here? (You can upload only first 1000 lines)

from fastp.

I'll test fastp again. I attached 1000 reads of E.coli data, but you can find plenty more publicly available, e.g.
https://github.com/nanopore-wgs-consortium/NA12878
nanopore.fastq.gz

from fastp.

fastp works fine now!

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