ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES terminated with an error exit status (8)
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Description
I have an issue with some but not all of the individuals I try to run: Of the 90 individuals 30 completed and the rest have the error below:
nextflow run pgscatalog/pgsc_calc -profile singularity --input samplesheet.csv \
--pgs_id PGS000614,PGS000071,PGS000152,PGS000607,PGS000615,PGS000616,PGS000723,PGS000782,PGS001807 \
--target_build GRCh38 --min_overlap 0.0 \
--liftover \
--hg19_chain /path/to/Test1/hg19ToHg38.over.chain.gz \
--hg38_chain /path/to/Test1/hg38ToHg19.over.chain.gz \
--run_ancestry /path/to/Test1/pgsc_HGDP+1kGP_v1.tar.zst \
--outdir BA1969B_output_blad-id \
--scorefile BA1969B_output-blad-id
N E X T F L O W ~ version 23.10.0
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [205cbfd1f5]
Launching `https://github.com/pgscatalog/pgsc_calc` [friendly_heisenberg] DSL2 - revision: 9bd9c431e7 [main]
WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: nf-schema@2.0.0,nf-prov@1.2.2
WARN: configuration option `validation.showHiddenParams` is deprecated, please use `validation.help.showHidden` or the `--showHidden` parameter instead
------------------------------------------------------
pgscatalog/pgsc_calc v2.0.0-beta.3-g9bd9c43
------------------------------------------------------
Core Nextflow options
revision : main
runName : friendly_heisenberg
containerEngine: singularity
launchDir : /path/PRS_test_2/Sample_BA1969B
workDir : /pathPRS_test_2/Sample_BA1969B/work
projectDir : /path/.nextflow/assets/pgscatalog/pgsc_calc
userName : zvaksman
profile : singularity
configFiles :
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use pgscatalog/pgsc_calc for your analysis please cite:
* The Polygenic Score Catalog
https://doi.org/10.1101/2024.05.29.24307783
https://doi.org/10.1038/s41588-021-00783-5
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/pgscatalog/pgsc_calc/blob/main/CITATIONS.md
Reference database provided: skipping bootstrap
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
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[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
Pulling Singularity image oras://ghcr.io/pgscatalog/plink2:2.00a5.10-singularity [cache /path/PRS_test_2/Sample_BA1969B/work/singularity/ghcr.io-pgscatalog-plink2-2.00a5.10-singularity.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /path/PRS_test_2/Sample_BA1969B/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
executor > local (1)
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
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[a0/c08c3b] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
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[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
Pulling Singularity image oras://ghcr.io/pgscatalog/plink2:2.00a5.10-singularity [cache /path/PRS_test_2/Sample_BA1969B/work/singularity/ghcr.io-pgscatalog-plink2-2.00a5.10-singularity.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /path/PRS_test_2/Sample_BA1969B/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
executor > local (1)
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
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[a0/c08c3b] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
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[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
Pulling Singularity image oras://ghcr.io/pgscatalog/plink2:2.00a5.10-singularity [cache /path/PRS_test_2/Sample_BA1969B/work/singularity/ghcr.io-pgscatalog-plink2-2.00a5.10-singularity.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /path/PRS_test_2/Sample_BA1969B/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
executor > local (2)
[e4/b66695] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
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[a0/c08c3b] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
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executor > local (2)
[e4/b66695] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
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[a0/c08c3b] process > PGSCATALOG_PGSCCALC:PGSCCAL... [100%] 1 of 1 ✔
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
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[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
executor > local (2)
[e4/b66695] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
[a0/c08c3b] process > PGSCATALOG_PGSCCALC:PGSCCAL... [100%] 1 of 1 ✔
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610, pgp_id:, trait_efo:])'
Caused by:
Process `PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610, pgp_id:, trait_efo:])` terminated with an error exit status (8)
Command executed:
pgscatalog-download -i PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610 -b GRCh38 -o $PWD -v -c pgsc_calc/2.0.0-beta.3
cat <<-END_VERSIONS > versions.yml
DOWNLOAD_SCOREFILES:
pgscatalog.core: $(echo $(python -c 'import pgscatalog.core; print(pgscatalog.core.__version__)'))
END_VERSIONS
Command exit status:
8
Command output:
(empty)
Command error:
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 478, in __call__
result = fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/_download.py", line 83, in ftp_fallback
raise ScoreDownloadError(f"Can't download {ftp_url} over FTP") from download_exc
pgscatalog.core.lib.pgsexceptions.ScoreDownloadError: Can't download ftp://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000615/ScoringFiles/Harmonized/PGS000615_hmPOS_GRCh38.txt.gz over FTP
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/app/pgscatalog.utils/.venv/bin/pgscatalog-download", line 8, in <module>
sys.exit(run())
^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/cli/download_cli.py", line 61, in run
future.result()
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 449, in result
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/usr/local/lib/python3.11/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/scorefiles.py", line 399, in download
https_download(
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 336, in wrapped_f
return copy(f, *args, **kw)
^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 475, in __call__
do = self.iter(retry_state=retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 376, in iter
result = action(retry_state)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 336, in wrapped_f
return copy(f, *args, **kw)
^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 475, in __call__
do = self.iter(retry_state=retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 376, in iter
result = action(retry_state)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/_download.py", line 30, in score_download_failed
raise ScoreDownloadError("All download retries failed") from download_exc
pgscatalog.core.lib.pgsexceptions.ScoreDownloadError: All download retries failed
Work dir:
/path/PRS_test_2/Sample_BA1969B/work/e4/b66695cfed8ad74b5d7a3496f706ba
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
executor > local (3)
[e4/b66695] process > PGSCATALOG_PGSCCALC:PGSCCAL... [100%] 1 of 1, failed: 1 ✘
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[17/3b4961] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
[a0/c08c3b] process > PGSCATALOG_PGSCCALC:PGSCCAL... [100%] 1 of 1 ✔
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
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[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610, pgp_id:, trait_efo:])'
Caused by:
Process `PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610, pgp_id:, trait_efo:])` terminated with an error exit status (8)
Command executed:
pgscatalog-download -i PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610 -b GRCh38 -o $PWD -v -c pgsc_calc/2.0.0-beta.3
cat <<-END_VERSIONS > versions.yml
DOWNLOAD_SCOREFILES:
pgscatalog.core: $(echo $(python -c 'import pgscatalog.core; print(pgscatalog.core.__version__)'))
END_VERSIONS
Command exit status:
8
Command output:
(empty)
Command error:
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 478, in __call__
result = fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/_download.py", line 83, in ftp_fallback
raise ScoreDownloadError(f"Can't download {ftp_url} over FTP") from download_exc
pgscatalog.core.lib.pgsexceptions.ScoreDownloadError: Can't download ftp://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000615/ScoringFiles/Harmonized/PGS000615_hmPOS_GRCh38.txt.gz over FTP
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/app/pgscatalog.utils/.venv/bin/pgscatalog-download", line 8, in <module>
sys.exit(run())
^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/cli/download_cli.py", line 61, in run
future.result()
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 449, in result
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/usr/local/lib/python3.11/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/scorefiles.py", line 399, in download
https_download(
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 336, in wrapped_f
return copy(f, *args, **kw)
^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 475, in __call__
do = self.iter(retry_state=retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 376, in iter
result = action(retry_state)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 336, in wrapped_f
return copy(f, *args, **kw)
^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 475, in __call__
do = self.iter(retry_state=retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 376, in iter
result = action(retry_state)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/_download.py", line 30, in score_download_failed
raise ScoreDownloadError("All download retries failed") from download_exc
pgscatalog.core.lib.pgsexceptions.ScoreDownloadError: All download retries failed
Work dir:
/path/PRS_test_2/Sample_BA1969B/work/e4/b66695cfed8ad74b5d7a3496f706ba
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
executor > local (3)
[e4/b66695] process > PGSCATALOG_PGSCCALC:PGSCCAL... [100%] 1 of 1, failed: 1 ✘
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[17/3b4961] process > PGSCATALOG_PGSCCALC:PGSCCAL... [100%] 1 of 1 ✔
[a0/c08c3b] process > PGSCATALOG_PGSCCALC:PGSCCAL... [100%] 1 of 1 ✔
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
Execution cancelled -- Finishing pending tasks before exit
-[pgscatalog/pgsc_calc] Pipeline completed with errors-
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610, pgp_id:, trait_efo:])'
Caused by:
Process `PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610, pgp_id:, trait_efo:])` terminated with an error exit status (8)
Command executed:
pgscatalog-download -i PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610 -b GRCh38 -o $PWD -v -c pgsc_calc/2.0.0-beta.3
cat <<-END_VERSIONS > versions.yml
DOWNLOAD_SCOREFILES:
pgscatalog.core: $(echo $(python -c 'import pgscatalog.core; print(pgscatalog.core.__version__)'))
END_VERSIONS
Command exit status:
8
Command output:
(empty)
Command error:
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 478, in __call__
result = fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/_download.py", line 83, in ftp_fallback
raise ScoreDownloadError(f"Can't download {ftp_url} over FTP") from download_exc
pgscatalog.core.lib.pgsexceptions.ScoreDownloadError: Can't download ftp://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000615/ScoringFiles/Harmonized/PGS000615_hmPOS_GRCh38.txt.gz over FTP
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/app/pgscatalog.utils/.venv/bin/pgscatalog-download", line 8, in <module>
sys.exit(run())
^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/cli/download_cli.py", line 61, in run
future.result()
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 449, in result
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/usr/local/lib/python3.11/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/scorefiles.py", line 399, in download
https_download(
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 336, in wrapped_f
return copy(f, *args, **kw)
^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 475, in __call__
do = self.iter(retry_state=retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 376, in iter
result = action(retry_state)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 336, in wrapped_f
return copy(f, *args, **kw)
^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 475, in __call__
do = self.iter(retry_state=retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 376, in iter
result = action(retry_state)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/_download.py", line 30, in score_download_failed
raise ScoreDownloadError("All download retries failed") from download_exc
pgscatalog.core.lib.pgsexceptions.ScoreDownloadError: All download retries failed
Work dir:
/path/PRS_test_2/Sample_BA1969B/work/e4/b66695cfed8ad74b5d7a3496f706ba
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
executor > local (3)
[e4/b66695] process > PGSCATALOG_PGSCCALC:PGSCCAL... [100%] 1 of 1, failed: 1 ✘
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... [ 0%] 0 of 1
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[17/3b4961] process > PGSCATALOG_PGSCCALC:PGSCCAL... [100%] 1 of 1 ✔
[a0/c08c3b] process > PGSCATALOG_PGSCCALC:PGSCCAL... [100%] 1 of 1 ✔
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[- ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
Execution cancelled -- Finishing pending tasks before exit
-[pgscatalog/pgsc_calc] Pipeline completed with errors-
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610, pgp_id:, trait_efo:])'
Caused by:
Process `PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610, pgp_id:, trait_efo:])` terminated with an error exit status (8)
Command executed:
pgscatalog-download -i PGS000614 PGS000071 PGS000152 PGS000607 PGS000615 PGS000616 PGS000723 PGS000782 PGS001807 PGS002017 PGS000608 PGS003335 PGS003736 PGS004241 PGS004687 PGS000609 PGS000610 -b GRCh38 -o $PWD -v -c pgsc_calc/2.0.0-beta.3
cat <<-END_VERSIONS > versions.yml
DOWNLOAD_SCOREFILES:
pgscatalog.core: $(echo $(python -c 'import pgscatalog.core; print(pgscatalog.core.__version__)'))
END_VERSIONS
Command exit status:
8
Command output:
(empty)
Command error:
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 478, in __call__
result = fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/_download.py", line 83, in ftp_fallback
raise ScoreDownloadError(f"Can't download {ftp_url} over FTP") from download_exc
pgscatalog.core.lib.pgsexceptions.ScoreDownloadError: Can't download ftp://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000615/ScoringFiles/Harmonized/PGS000615_hmPOS_GRCh38.txt.gz over FTP
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/app/pgscatalog.utils/.venv/bin/pgscatalog-download", line 8, in <module>
sys.exit(run())
^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/cli/download_cli.py", line 61, in run
future.result()
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 449, in result
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/usr/local/lib/python3.11/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/scorefiles.py", line 399, in download
https_download(
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 336, in wrapped_f
return copy(f, *args, **kw)
^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 475, in __call__
do = self.iter(retry_state=retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 376, in iter
result = action(retry_state)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 336, in wrapped_f
return copy(f, *args, **kw)
^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 475, in __call__
do = self.iter(retry_state=retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/tenacity/__init__.py", line 376, in iter
result = action(retry_state)
^^^^^^^^^^^^^^^^^^^
File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/core/lib/_download.py", line 30, in score_download_failed
raise ScoreDownloadError("All download retries failed") from download_exc
pgscatalog.core.lib.pgsexceptions.ScoreDownloadError: All download retries failed
Work dir:
/path/PRS_test_2/Sample_BA1969B/work/e4/b66695cfed8ad74b5d7a3496f706ba
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
```Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by rerunning the posted Nextflow command and inspect the complete failure output for the PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES process, including its work directory. The report only shows exit status 8 and a truncated log, so done requires reproducing the failure, identifying why only some individuals fail, and verifying a fix across the affected inputs.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, devops
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100