subprocess.CalledProcessError: Command 'pairix /home/zjin/neat1/13.TAD_boundary_pile_up/mcool/.HiCLift/c2c12.pairs.gz' returned non-zero exit status 127.

[gavinjzg]

Hi！
I am facing an issuea bout the output format.
when i use the pairs ,it's ok.

but when i use the hic ,It shows an error like subprocess.CalledProcessError: Command 'pairix /home/zjin/neat1/13.TAD_boundary_pile_up/mcool/.pairliftover/c2c12.pairs.gz' returned non-zero exit status 127
(peakachu) HiCLift --input test.mm10.100kb.cool --input-format cooler --out-pre c2c12 --output-format hic --out-chromsizes ./new_mm10_gsize_NoMTY --in-assembly mm21 --out-assembly mm21 --memory 40G
root INFO @ 05/05/23 14:41:29:

ARGUMENT LIST:

Input path = test.mm10.100kb.cool

Input format = cooler

Output prefix = c2c12

Output format = hic

Chromosome Sizes of the output assembly = ./new_mm10_gsize_NoMTY

Generate contact maps at 11 resolutions = False

Input assembly = mm21

Output assembly = mm21

Chain file = None

Temporary Dir = .HiCLift

Allocated memory = 40G

Number of Processes = 8

Log file name = HiCLift.log

root INFO @ 05/05/23 14:41:39: Trying to perform a pure format conversion without liftover ...
HiCLift.utilities INFO @ 05/05/23 14:41:39: Writing headers ...
HiCLift.utilities INFO @ 05/05/23 14:41:39: Dumping contact pairs from test.mm10.100kb.cool ...
/bin/sh: pairix: command not found
Traceback (most recent call last):
File "/home/zjin/anaconda3/envs/peakachu/bin/HiCLift", line 137, in
run()
File "/home/zjin/anaconda3/envs/peakachu/bin/HiCLift", line 110, in run
liftover(
File "/home/zjin/anaconda3/envs/peakachu/lib/python3.8/site-packages/HiCLift/utilities.py", line 213, in liftover
subprocess.check_call(' '.join(command), shell=True)
File "/home/zjin/anaconda3/envs/peakachu/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'pairix /home/zjin/neat1/13.TAD_boundary_pile_up/mcool/.HiCLift/c2c12.pairs.gz' returned non-zero exit status 127.
How should I solve this problem?Thank you for your help and time,

[XiaoTaoWang]

Hi, the error message indicates that the pairix command cannot be found. Have you installed HiCLift according to the guidelines provided here https://github.com/XiaoTaoWang/HiCLift#installation?