Unable to run plinkliftover liftover in a remote server. Error: No such command ...

[MrLocuace]

I installed plinkliftover in a remote server (Python 3.8.5):

pip install -U plinkliftover

I run this command:

plinkliftover liftover chile271samples.snps.2alleles.maf0.01.c1_22.norm.map /project/he/USERS/me/czi/data/liftover/hg19ToHg38.over.chain.gz --prefix chile271.8MM.hg38 --liftoverexecutable /home/me/.local/bin/plinkliftover

I get:

[me@midway3-login4 chile.all]$ plinkliftover liftover chile271samples.snps.2alleles.maf0.01.c1_22.norm.map /project/he/USERS/me/czi/data/liftover/hg19ToHg38.over.chain.gz --prefix chile271.8MM.hg38 --liftoverexecutable /home/me/.local/bin/plinkliftover
Converting MAP file chile271samples.snps.2alleles.maf0.01.c1_22.norm.map file to UCSC BED file chile271samples.snps.2alleles.maf0.01.c1_22.norm.bed...
[####################################] 100%
Lifting BED file chile271samples.snps.2alleles.maf0.01.c1_22.norm.bed...
Usage: plinkliftover [OPTIONS] COMMAND [ARGS]...
Try 'plinkliftover --help' for help.

Error: No such command 'chile271samples.snps.2alleles.maf0.01.c1_22.norm.bed'.
Traceback (most recent call last):
File "/home/me/.local/bin/plinkliftover", line 8, in
sys.exit(app())
File "/home/me/.local/lib/python3.8/site-packages/typer/main.py", line 214, in call
return get_command(self)(*args, **kwargs)
File "/software/python-anaconda-2020.11-el8-x86_64/lib/python3.8/site-packages/click/core.py", line 1128, in call
return self.main(*args, **kwargs)
File "/software/python-anaconda-2020.11-el8-x86_64/lib/python3.8/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/software/python-anaconda-2020.11-el8-x86_64/lib/python3.8/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/software/python-anaconda-2020.11-el8-x86_64/lib/python3.8/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/software/python-anaconda-2020.11-el8-x86_64/lib/python3.8/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/home/me/.local/lib/python3.8/site-packages/typer/main.py", line 532, in wrapper
return callback(**use_params) # type: ignore
File "/home/me/.local/lib/python3.8/site-packages/plinkliftover/main.py", line 80, in liftover
lifted_set, unlifted_set, lb_status = liftBed(
File "/home/me/.local/lib/python3.8/site-packages/plinkliftover/liftover.py", line 47, in liftBed
check_output(params.values())
File "/software/python-anaconda-2020.11-el8-x86_64/lib/python3.8/subprocess.py", line 411, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/software/python-anaconda-2020.11-el8-x86_64/lib/python3.8/subprocess.py", line 512, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'dict_values([PosixPath('/home/lucasvicuna82/.local/bin/plinkliftover'), PosixPath('chile271samples.snps.2alleles.maf0.01.c1_22.norm.bed'), '/project/he/USERS/me/czi/data/liftover/hg19ToHg38.over.chain.gz', PosixPath('chile271samples.snps.2alleles.maf0.01.c1_22.norm.map.bed'), 'chile271samples.snps.2alleles.maf0.01.c1_22.norm.map.bed.unlifted'])' returned non-zero exit status 2.

I have tried many different modifications in the script, but none of them work.

Please help

[github-actions]

Hello @MrLocuace, thank you for your interest in our work!

If this is a bug report, please provide screenshots and minimum viable code to reproduce your issue, otherwise we can not help you.

[MrLocuace]

Hello,
I did provide the code and the content of the screenshots

[MrLocuace]

Could you please provide me an email address to I can share the files privately?
Thank you