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XiaoTaoWang / HiCLift

A fast and efficient tool for converting chromatin interaction data between genome assemblies
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subprocess.CalledProcessError: Command 'pairix /home/zjin/neat1/13.TAD_boundary_pile_up/mcool/.HiCLift/c2c12.pairs.gz' returned non-zero exit status 127. #12

Open gavinjzg opened 1 year ago

gavinjzg commented 1 year ago

Hi！ I am facing an issuea bout the output format. when i use the pairs ,it's ok. image 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 commented 1 year ago

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?