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Problem with download_hg_reference

Open hsun3163 opened this issue 2 years ago • 1 comments

While running sos run pipeline/reference_data.ipynb download_hg_reference --cwd reference_data in the login node, following error occurs.

hs3163@csglogin:/mnt/vast/hpc/csg/xqtl_workflow_testing/finalizing/reference_data$
GRCh38_ful...lus_decoy_hla.fa: <urlopen error ftp error: TimeoutError(110, 'Connection timed out')>:
ERROR: download_hg_reference (id=c29278acf831fdde) returns an error.
ERROR: [download_hg_reference]: [0]:
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
script_4737362758465142950 in <module>
----> download('ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa\n\n', dest_dir = cwd)


RuntimeError: Failed to download {urls[0]}

[1]+  Exit 1                  sos run pipeline/reference_data.ipynb download_hg_reference --cwd reference_data  (wd: /mnt/vast/hpc/csg/xqtl_workflow_testing/finalizing)

hsun3163 avatar Sep 08 '22 22:09 hsun3163