# Kneaddata final pair output is 0

**URL:** <https://forum.biobakery.org/t/kneaddata-final-pair-output-is-0/7548>\
**Category:** KneadData\
**Created:** [November 5, 2024, 4:23pm UTC](https://forum.biobakery.org/t/kneaddata-final-pair-output-is-0/7548 "2024-11-05T16:23:17Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![weichi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/weichi/32/3118_2.png) [@weichi](https://forum.biobakery.org/u/weichi)\
**Post date:** [December 25, 2024, 3:41am UTC](https://forum.biobakery.org/t/kneaddata-final-pair-output-is-0/7548/2 "2024-12-25T03:41:45Z")

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Hi, this issue seems to have already been discussed in another topic.  
You can try out those solutions.

> [@All paired-end read unmatched](https://forum.biobakery.org/t/all-paired-end-read-unmatched/2895/36):
>
> Here is the installation command based on @EacoChen’s comment, which can resolve this issue: git clone https://github.com/biobakery/kneaddata \ && cd kneaddata \ && git reset --hard ebc077999b7d020f666a11aec782119ab764e00f \ # the commit I use is 90c05f3cd25a8c74a4d804f27dd0ce52718007d8 && python3 setup.py install --bypass-dependencies-install

> [@All paired-end read unmatched](https://forum.biobakery.org/t/all-paired-end-read-unmatched/2895/35):
>
> If anyone is still facing this issue and doesn’t want to modify the utility.py file, you can use the following shell one-liner as a workaround. The issue arises because the following code block, which was present in version 0.10.0, is missing from the utility.py file in version 0.12.0: with open(new\_file, "wt") as file\_handle: for lines in read\_file\_n\_lines(file,4): # Reformat the identifier and write to the temp file if " 1:" in lines[0]: lines[0] = lines[0].re…

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