PRSice 2 error

Hi!

Has anyone encountered this error while running the built-in PRSice 2 tool? The reading of the --base summary statistics seems to get truncated, and I can’t pinpoint why.

Some context:

• The summary stats file has 1,525,733 rows and is tab-delimited.
• I’ve tried splitting it into multiple smaller files, but it consistently fails around 4.8% of reading.

I’d greatly appreciate any suggestions on what might be causing this truncation. 

/opt/PRSice_linux \
 --a1 alt \
 --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \
 --base filtered_unique.tsv \
 --binary-target F \
 --clump-kb 250kb \
 --clump-p 1.0 \
 --clump-r2 0.1 \
 --interval 5e-05 \
 --lower 5e-08 \
 --num-auto 22 \
 --or \
 --out filtered_unique \
 --pvalue pval \
 --seed 3422831479 \
 --snp rsids \
 --stat OR \
 --target target \
 --thread 16 \
 --upper 0.5

Initializing Genotype file: target (bed) Start processing filtered_unique ================================================== 

Base file: filtered_unique.tsv 

Header of file is: chrom pos ref alt rsids pval beta OR 

Reading 0.01%

Reading 0.02%

Reading 0.03%

Reading 0.04%

….

Reading 4.58% Read... [truncated]

Traceback (most recent call last):

  File "/home/dnanexus/job-J4Q16BjJqV0zGKvzgZ7vvjVJ", line 39, in <module>

    exec_code(job_code, _code_filename)

  File "/home/dnanexus/job-J4Q16BjJqV0zGKvzgZ7vvjVJ", line 25, in exec_code

    exec(compiled_code, globals())

  File "/home/dnanexus/job-J4Q16BjJqV0zGKvzgZ7vvjVJ.code.py", line 128, in <module>

    dxpy.run()

  File "/usr/local/lib/python3.12/dist-packages/dxpy/utils/exec_utils.py", line 131, in run

    result = ENTRY_POINT_TABLE[job['function']](**job['input'])

             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/dnanexus/job-J4Q16BjJqV0zGKvzgZ7vvjVJ.code.py", line 111, in main

    get_docker().run(cmd)

  File "/usr/lib/python3/dist-packages/sugar/dockertools.py", line 347, in run

    self._handle_last_process_cpe(cpe)

  File "/usr/lib/python3/dist-packages/sugar/dockertools.py", line 368, in _handle_last_process_cpe

    raise cpe

  File "/usr/lib/python3/dist-packages/sugar/dockertools.py", line 337, in run

    self._last_process = processing.run(

                         ^^^^^^^^^^^^^^^

  File "/usr/lib/python3/dist-packages/sugar/processing/__init__.py", line 122, in run

    processes.block()

  File "/usr/lib/python3/dist-packages/sugar/processing/core.py", line 462, in block

    self.raise_if_error()

  File "/usr/lib/python3/dist-packages/sugar/processing/core.py", line 576, in raise_if_error

    raise CalledProcessError(self.returncode, str(self), output=msg)

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 filtered_unique.tsv --target target --thread 16 --out filtered_unique --stat OR --binary-target T --snp rsids --a1 alt --pvalue pval --binary-target F --or'' returned non-zero exit status 1.