Immune Repertoire pipeline and SHM & CSR pipeline (ARGalaxy): Error with tutorial data

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Hi,
I am new at using Galaxy and trying to follow the tutorials of Immune Repertoire pipeline and SHM & CSR pipeline using tutorial test data sets. But the analyses ended up with some errors as below. How can I fix these??
Thanks,

ERROR from Immune Repertoire pipeline:

cat: /var/lib/galaxy/database/jobs_directory/008/8936/dataset_656640_files/samples.txt: No such file or directory
/var/lib/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/davidvanzessen/argalaxy_tools/33412e85e669/argalaxy_tools/report_clonality/r_wrapper.sh: line 55: /var/lib/galaxy/database/jobs_directory/008/8936/dataset_656640_files/productive_counting.txt: No such file or directory
/var/lib/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/davidvanzessen/argalaxy_tools/33412e85e669/argalaxy_tools/report_clonality/r_wrapper.sh: line 149: /var/lib/galaxy/database/jobs_directory/008/8936/dataset_656640_files/AAMedianBySample.txt: No such file or directory
/var/lib/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/davidvanzessen/argalaxy_tools/33412e85e669/argalaxy_tools/report_clonality/r_wrapper.sh: line 344: 7za: command not found
/var/lib/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/davidvanzessen/argalaxy_tools/33412e85e669/argalaxy_tools/report_clonality/r_wrapper.sh: line 350: 7za: command not found

ERROR from SHM & CSR pipeline:

/var/lib/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/davidvanzessen/shm_csr/f387cc1580c6/shm_csr/baseline/script_imgt.py:20: DeprecationWarning: 'U' mode is deprecated
  with open(args.ref, 'rU') as ref:
/var/lib/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/davidvanzessen/shm_csr/f387cc1580c6/shm_csr/baseline/script_imgt.py:20: DeprecationWarning: 'U' mode is deprecated
  with open(args.ref, 'rU') as ref:
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On which galaxy server are you working? Is it perhaps this one? https://argalaxy.researchlumc.nl/

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Yes Iā€™m using that server

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Then you may get a better and faster response if you contact that maintainer. The error looks like some technical issues but I can never be sure.

1 Like
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Thanks a lot!