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ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES terminated with an error exit status (8) #391

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vaksmaz opened this issue Nov 19, 2024 · 1 comment
Open

ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES terminated with an error exit status (8) #391

vaksmaz opened this issue Nov 19, 2024 · 1 comment

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@vaksmaz
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vaksmaz commented Nov 19, 2024

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NOTE: Your local project version looks outdated - a different revision is available in the remote repository [205cbfd1f5]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: [email protected],[email protected]
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... -
[-        ] 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... -
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[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] 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... -
[-        ] 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... -
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[-        ] 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... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -

[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] 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... -
[-        ] 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... -
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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[-        ] 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... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] 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... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] 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... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
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[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] 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... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] 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
[-        ] 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... -
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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... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] 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... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCAL... -
[-        ] 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... -
[-        ] 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
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
```
@vaksmaz
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vaksmaz commented Nov 19, 2024

Sorry, wrong spot, this was an accident and I can't remove it. This is not for you guys

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