nchari
November 5, 2024, 4:23pm
1
When running biobakery workflows with paired end reads, my paired end reads are recognized by kneaddata, but the final pair values are 0 across the board, with all the reads showing up as orphan reads? Any info on why this would be the case?
weichi
December 25, 2024, 3:41am
2
Hi, this issue seems to have already been discussed in another topic.
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
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…
