prsice2 in CLI
I am currently using prsice
in the CLI for PRS analysis, and here is my job log. I would like to know how to properly configure the target
parameter content. I haven't seen any prompts asking for target
input during the operation; it only requires the input of bed
, fim
, and bim
files. Since the bfile
I received is divided by chromosomes, I am considering using a target list
instead of target
. If it is necessary to use target
, please tell me how to proceed.
my job log
Job ID: job-GvYbPf8Jb1yJBGpZyPXQ93vg
Watch launched job now? [Y/n] Y
Job Log
-------
Watching job job-GvYbPf8Jb1yJBGpZyPXQ93vg. Press Ctrl+C to stop watching.
* PRSice 2 (prsice2:main) (running) job-GvYbPf8Jb1yJBGpZyPXQ93vg
mouyonggao 2024-11-03 19:00:41 (running for 0:01:19)
2024-11-03 19:02:47 PRSice 2 INFO Logging initialized (priority)
2024-11-03 19:02:47 PRSice 2 INFO Logging initialized (bulk)
2024-11-03 19:02:51 PRSice 2 INFO Downloading bundled file resources.tar.gz
2024-11-03 19:02:54 PRSice 2 STDOUT >>> Unpacking resources.tar.gz to /
2024-11-03 19:02:54 PRSice 2 STDERR tar: Removing leading `/' from member names
2024-11-03 19:02:56 PRSice 2 STDOUT dxpy/0.383.1 (Linux-5.15.0-1071-aws-x86_64-with-glibc2.29) Python/3.8.10
2024-11-03 19:02:57 PRSice 2 STDOUT Invoking main with {'base_assoc': {'$dnanexus_link': 'file-GvY5XXQJb1yBQKV9434y8GjB'}, 'plink_bed': {'$dnanexus_link': 'file-GvYZzyjJb1y4k2k7vXQfjYyb'}, 'plink_bim': {'$dnanexus_link': 'file-GvYZzyjJb1y4k2k7vXQfjYyb'}, 'plink_fam': {'$dnanexus_link': 'file-GvYZzyjJb1y4k2k7vXQfjYyb'}, 'pheno_txt': {'$dnanexus_link': 'file-GvYb5x0Jb1y4Vx3QxPpYBYp4'}, 'trait': 'binary', 'extra_options': '--a1 A1 --a2 A2 --pvalue P --stat OR --or --clump-kb 250kb --clump-p 1.000000 --clump-r2 0.1 --target-list ukbfile_full.txt', 'gen_plots': True}
2024-11-03 19:02:57 PRSice 2 INFO Downloading file file-GvY5XXQJb1yBQKV9434y8GjB to /home/dnanexus/PRSbase.tsv
2024-11-03 19:02:57 PRSice 2 INFO Downloading file file-GvYZzyjJb1y4k2k7vXQfjYyb to /home/dnanexus/ukbfile_full.txt
2024-11-03 19:02:57 PRSice 2 INFO Downloading file file-GvYZzyjJb1y4k2k7vXQfjYyb to /home/dnanexus/ukbfile_full.txt
2024-11-03 19:02:57 PRSice 2 INFO Downloading file file-GvYb5x0Jb1y4Vx3QxPpYBYp4 to /home/dnanexus/pheno.tsv
2024-11-03 19:02:57 PRSice 2 INFO Downloading file file-GvYZzyjJb1y4k2k7vXQfjYyb to /home/dnanexus/ukbfile_full.txt
2024-11-03 19:02:58 PRSice 2 INFO Completed downloading file file-GvY5XXQJb1yBQKV9434y8GjB to /home/dnanexus/PRSbase.tsv
2024-11-03 19:02:58 PRSice 2 INFO Completed downloading file file-GvYZzyjJb1y4k2k7vXQfjYyb to /home/dnanexus/ukbfile_full.txt
2024-11-03 19:02:58 PRSice 2 INFO Completed downloading file file-GvYZzyjJb1y4k2k7vXQfjYyb to /home/dnanexus/ukbfile_full.txt
2024-11-03 19:02:58 PRSice 2 INFO Completed downloading file file-GvYZzyjJb1y4k2k7vXQfjYyb to /home/dnanexus/ukbfile_full.txt
2024-11-03 19:02:58 PRSice 2 INFO Completed downloading file file-GvYb5x0Jb1y4Vx3QxPpYBYp4 to /home/dnanexus/pheno.tsv
2024-11-03 19:02:58 PRSice 2 INFO Input files: {'base_assoc': PosixPath('/home/dnanexus/PRSbase.tsv'), 'plink_bed': PosixPath('/home/dnanexus/ukbfile_full.txt'), 'plink_bim': PosixPath('/home/dnanexus/ukbfile_full.txt'), 'plink_fam': PosixPath('/home/dnanexus/ukbfile_full.txt'), 'pheno_txt': PosixPath('/home/dnanexus/pheno.tsv')}
2024-11-03 19:02:58 PRSice 2 INFO Output prefix: PRSbase
2024-11-03 19:03:05 PRSice 2 INFO Running: Rscript /opt/PRSice.R --prsice /opt/PRSice_linux --base PRSbase.tsv --target target --thread 8 --out PRSbase --pheno pheno.tsv --stat OR --binary-target T --a1 A1 --a2 A2 --pvalue P --stat OR --or --clump-kb 250kb --clump-p 1.000000 --clump-r2 0.1 --target-list ukbfile_full.txt
2024-11-03 19:03:07 PRSice 2 ERROR stderr from executed commands:
PRSice 2.3.5 (2021-09-20)
https://github.com/choishingwan/PRSice
(C) 2016-2020 Shing Wan (Sam) Choi and Paul F. O'Reilly
GNU General Public License v3
If you use PRSice in any published work, please cite:
Choi SW, O'Reilly PF.
PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data.
GigaScience 8, no. 7 (July 1, 2019)
2024-11-03 11:03:06
/opt/PRSice_linux \
--a1 A1 \
--a2 A2 \
--bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \
--base PRSbase.tsv \
--base-info INFO:0.9 \
--binary-target T \
--clump-kb 250kb \
--clump-p 1.000000 \
--clump-r2 0.100000 \
--interval 5e-05 \
--lower 5e-08 \
--num-auto 22 \
--or \
--out PRSbase \
--pheno pheno.tsv \
--pvalue P \
--seed 2806816404 \
--snp SNP \
--stat OR \
--target target \
--target-list ukbfile_full.txt \
--thread 8 \
--upper 0.5
Error: You can only use --target or --target-list but not
both
Error: You can only use --target or --target-list but not both
Error:
Execution halted
2024-11-03 19:03:07 PRSice 2 STDERR Traceback (most recent call last):
2024-11-03 19:03:07 PRSice 2 STDERR File "/home/dnanexus/job-GvYbPf8Jb1yJBGpZyPXQ93vg", line 39, in <module>
2024-11-03 19:03:07 PRSice 2 STDERR exec_code(job_code, _code_filename)
2024-11-03 19:03:07 PRSice 2 STDERR File "/home/dnanexus/job-GvYbPf8Jb1yJBGpZyPXQ93vg", line 25, in exec_code
2024-11-03 19:03:07 PRSice 2 STDERR exec(compiled_code, globals())
2024-11-03 19:03:07 PRSice 2 STDERR File "/home/dnanexus/job-GvYbPf8Jb1yJBGpZyPXQ93vg.code.py", line 128, in <module>
2024-11-03 19:03:07 PRSice 2 STDERR dxpy.run()
2024-11-03 19:03:07 PRSice 2 STDERR File "/usr/local/lib/python3.8/dist-packages/dxpy/utils/exec_utils.py", line 150, in run
2024-11-03 19:03:07 PRSice 2 STDERR result = ENTRY_POINT_TABLE[job['function']](**job['input'])
2024-11-03 19:03:07 PRSice 2 STDERR File "/home/dnanexus/job-GvYbPf8Jb1yJBGpZyPXQ93vg.code.py", line 111, in main
2024-11-03 19:03:07 PRSice 2 STDERR get_docker().run(cmd)
2024-11-03 19:03:07 PRSice 2 STDERR File "/usr/lib/python3/dist-packages/sugar/dockertools.py", line 347, in run
2024-11-03 19:03:07 PRSice 2 STDERR self._handle_last_process_cpe(cpe)
2024-11-03 19:03:07 PRSice 2 STDERR File "/usr/lib/python3/dist-packages/sugar/dockertools.py", line 368, in _handle_last_process_cpe
2024-11-03 19:03:07 PRSice 2 STDERR raise cpe
2024-11-03 19:03:07 PRSice 2 STDERR File "/usr/lib/python3/dist-packages/sugar/dockertools.py", line 337, in run
2024-11-03 19:03:07 PRSice 2 STDERR self._last_process = processing.run(
2024-11-03 19:03:07 PRSice 2 STDERR File "/usr/lib/python3/dist-packages/sugar/processing/__init__.py", line 122, in run
2024-11-03 19:03:07 PRSice 2 STDERR processes.block()
2024-11-03 19:03:07 PRSice 2 STDERR File "/usr/lib/python3/dist-packages/sugar/processing/core.py", line 462, in block
2024-11-03 19:03:07 PRSice 2 STDERR self.raise_if_error()
2024-11-03 19:03:07 PRSice 2 STDERR File "/usr/lib/python3/dist-packages/sugar/processing/core.py", line 576, in raise_if_error
2024-11-03 19:03:07 PRSice 2 STDERR raise CalledProcessError(self.returncode, str(self), output=msg)
2024-11-03 19:03:07 PRSice 2 STDERR subprocess.CalledProcessError: Command 'docker run -e PYTHONUNBUFFERED=s -v /home/dnanexus:/home/dnanexus -w /home/dnanexus --rm dnanexus/prsice2:latest bash -c 'Rscript /opt/PRSice.R --prsice /opt/PRSice_linux --base PRSbase.tsv --target target --thread 8 --out PRSbase --pheno pheno.tsv --stat OR --binary-target T --a1 A1 --a2 A2 --pvalue P --stat OR --or --clump-kb 250kb --clump-p 1.000000 --clump-r2 0.1 --target-list ukbfile_full.txt'' returned non-zero exit status 1.
* PRSice 2 (prsice2:main) (failed) job-GvYbPf8Jb1yJBGpZyPXQ93vg
mo 2024-11-03 19:00:41 (runtime 0:01:16)
AppInternalError: CalledProcessError: Command 'docker run -e PYTHONUNBUFFERED=s -v /home/dnanexus:/home/dnanexus -w
/home/dnanexus --rm dnanexus/prsice2:latest bash -c 'Rscript /opt/PRSice.R --prsice
/opt/PRSice_linux --base PRSbase.tsv --target target --thread 8 --out PRSbase --pheno pheno.tsv
--stat OR --binary-target T --a1 A1 --a2 A2 --pvalue P --stat OR --or --clump-kb 250kb --clump-p
1.000000 --clump-r2 0.1 --target-list ukbfile_full.txt'' returned non-zero exit status 1.
Comments
1 comment
Hi
If you wish to run prsice2 on all the individuals/positions available in one analysis I think using the --target-list may be the correct path. However, I would suggest reaching out to the authors of the program for advice on best practices.
Due to the large size of the UKBiobank data, it might be more cost effective to run any filters for quality, regions or individuals of interest before running prsice2.
Hope this helps, thank you for using the community forum.
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