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

**URL:** <https://help.galaxyproject.org/t/immune-repertoire-pipeline-and-shm-csr-pipeline-argalaxy-error-with-tutorial-data/9449>\
**Category:** Uncategorized\
**Tags:** gtn-tutorial, workflow, usinggalaxy\
**Created:** [February 12, 2023, 5:01pm UTC](https://help.galaxyproject.org/t/immune-repertoire-pipeline-and-shm-csr-pipeline-argalaxy-error-with-tutorial-data/9449 "2023-02-12T17:01:27Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![khani](https://avatars.discourse-cdn.com/v4/letter/k/3da27b/32.png) [@khani](https://help.galaxyproject.org/u/khani)\
**Post date:** [February 12, 2023, 5:01pm UTC](https://help.galaxyproject.org/t/immune-repertoire-pipeline-and-shm-csr-pipeline-argalaxy-error-with-tutorial-data/9449/1 "2023-02-12T17:01:28Z")

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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:

```auto
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:

```auto
/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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<div class="post-metadata">

**Author:** ![gbbio](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gbbio/32/366_2.png) [@gbbio](https://help.galaxyproject.org/u/gbbio)\
**Post date:** [February 13, 2023, 10:09am UTC](https://help.galaxyproject.org/t/immune-repertoire-pipeline-and-shm-csr-pipeline-argalaxy-error-with-tutorial-data/9449/2 "2023-02-13T10:09:08Z")

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On which galaxy server are you working? Is it perhaps this one? [https://argalaxy.researchlumc.nl/](https://argalaxy.researchlumc.nl/)

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**Author:** ![khani](https://avatars.discourse-cdn.com/v4/letter/k/3da27b/32.png) [@khani](https://help.galaxyproject.org/u/khani)\
**Post date:** [February 13, 2023, 12:40pm UTC](https://help.galaxyproject.org/t/immune-repertoire-pipeline-and-shm-csr-pipeline-argalaxy-error-with-tutorial-data/9449/3 "2023-02-13T12:40:42Z")

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Yes I’m using that server

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<div class="post-metadata">

**Author:** ![gbbio](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gbbio/32/366_2.png) [@gbbio](https://help.galaxyproject.org/u/gbbio)\
**Post date:** [February 14, 2023, 9:19am UTC](https://help.galaxyproject.org/t/immune-repertoire-pipeline-and-shm-csr-pipeline-argalaxy-error-with-tutorial-data/9449/4 "2023-02-14T09:19:48Z")

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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.

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<div class="post-metadata">

**Author:** ![khani](https://avatars.discourse-cdn.com/v4/letter/k/3da27b/32.png) [@khani](https://help.galaxyproject.org/u/khani)\
**Post date:** [February 17, 2023, 4:20am UTC](https://help.galaxyproject.org/t/immune-repertoire-pipeline-and-shm-csr-pipeline-argalaxy-error-with-tutorial-data/9449/5 "2023-02-17T04:20:20Z")

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Thanks a lot!

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [February 22, 2023, 6:52pm UTC](https://help.galaxyproject.org/t/immune-repertoire-pipeline-and-shm-csr-pipeline-argalaxy-error-with-tutorial-data/9449/6 "2023-02-22T18:52:19Z")

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