unrecognized option -- f

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Yuko Nakano

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Jun 14, 2023, 12:55:30 PM6/14/23

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Hello,

I installed PEAR a few years ago and it had worked well to pair forward and reverse reads until March of this year. At that time, the version was v0.9.6.

$ pear -f forward.fastq -r reverse.fastq -o output

However, when I ran the same command, I've gotten the following error message; "unrecognized option -- f". The version is now 1.10.13.

Is the problem the version 1.10.13 or are there any ways to solve this issue?

Amy Slender

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Sep 21, 2023, 9:24:17 PM9/21/23

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Hi Yuko, This issue was posted a while ago but I'm having the same issue and I have the solution so I thought I would reply in case it will help other people. I think the PEAR that you are referring to above is actually a different program to what you need (https://manpages.ubuntu.com/manpages/jammy/man1/pear.1.html).