umi_tools extract --> error saying 'extract' is not a UMI-tools command

[mdu4003]

Hello, I am using umi_tools v. 1.1.4 at HPC and the command: $ umi_tools extract --stdin=raw/MDU1.fastq --bc-pattern=NNNNNNNNN --log=processed.log --stdout=test.bam gives me this error:

'extract' is not a UMI-tools command. See 'umi_tools -h'.

For full UMI-tools documentation, see: https://umi-tools.readthedocs.io/en/latest/

umi_tools.py - Tools for UMI analyses

:Author: Tom Smith & Ian Sudbury, CGAT :Tags: Genomics UMI

There are 6 tools:

• whitelist
• extract
• group
• dedup
• count
• count_tab

To get help on a specific tool, type:

umi_tools <tool> --help

To use a specific tool, type::

umi_tools <tool> [tool options] [tool arguments]

Do you have any solution, please?

Thanks! Angeles

[mdu4003]

I installed it on my Mac, and it worked. But it is giving that error when I use it on HPC. Should I load anything else to be able to run it on HPC? This is my code: $ spack load py.umi_tools@ I even installed it, but it gave me the same error. Thanks!! Angeles

[IanSudbery]

This usually means that when umi_tools has looked for the code associated with the tool, it hasn't been able to find it.

I couple of possible reasons are:

• The code is not installed in the default location for python code and the PYTHONPATH environment variable has not been set to the location that does contain it.
• The system is using an unsupported version of python. UMI-tools requires python >= 3.5.

I don't really know anything about how the spack package manager works, so ifs difficult for me to offer further help.

On Wed, 27 Dec 2023 at 17:40, mdu4003 @.***> wrote:

I installed it on my Mac, and it worked. But it is giving that error when I use it on HPC. Should I load anything else to be able to run it on HPC? This is my code: $ spack load py.umi_tools@ I even installed it, but it gave me the same error. Thanks!! Angeles

— Reply to this email directly, view it on GitHub https://github.com/CGATOxford/UMI-tools/issues/620#issuecomment-1870503504, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABJELDVYRGEEKQLDOQY2MM3YLRMPPAVCNFSM6AAAAABBDXWKI6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZQGUYDGNJQGQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[TomSmithCGAT]

@mdu4003 - Closing now due to inactivity