prsice2 in CLI

Wang Lei

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

  • Comment author
    George F The helpers that keep the community running smoothly. UKB Community team Data Analyst

    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.

    0

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