'extract' is not a UMI-tools command.

[yueli8]

Hello,

It looks like that I have already installed UMI-tools, but extract does not work.

Thank you in advance for your great help!

Best,

Yue

-P330:~/UMI-tools-master$ umi_tools
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]

-P330:~/UMI-tools-master$ umi_tools extract
'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]

[IanSudbery]

This means that the PYTHONPATH isn't setup to look in the place where umi-tools is install.

I looked at the install log you posted a minute ago, and this caught my eye:

umi-tools 1.1.5 is already the active version in easy-install.pth

I wonder if its still looking in the python 2 location?

what do you get if you do

$ cat `which umi_tools`

[yueli8]

Hello IanSudbery,

Thank you so much for your quick response!

1. It seems that I have alredy installed umi_tools in /home/yueli/.local/bin/umi_tools.

P330:~$ which umi_tools
/home/yueli/.local/bin/umi_tools

2. Is that because I installed python 3.8 not python 3.7?

P330:~$ pip3 --version
pip 24.0 from /home/yueli/.local/lib/python3.8/site-packages/pip (python 3.8)

3. 'extract' is not a UMI-tools command in $ path

Thank you again and really appreciated your great help!

Best,

Yue

P330:~$ umi_tools
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]

yueli@yueli-ThinkStation-P330:~$ umi_tools extract
'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]

[IanSudbery]

Python 3.7 vs 3.8 shouldn't make any difference. However, UMI-tools will be linked to the python installed when it is installed. The "sheband" line at the start of the `/home/yueli/.local/bin/umi_tools` script will indicate which python it is trying to run from.

[tgbrooks]

For anyone else ending up here, I got this error message when pysam wasn't properly installed. Running pip install pysam fixed it.

[437364]

For me, specifying the absolute path to umi_tools seems to fix it

(tools) mkratka@pc-t7-094:/netscratch/dep_mercier/grp_marques/Marie/Luzula_sylvatica/data/scRNA$ umi_tools count
'count' 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]

(tools) mkratka@pc-t7-094:/netscratch/dep_mercier/grp_marques/Marie/Luzula_sylvatica/data/scRNA$ which umi_tools
/netscratch/dep_mercier/grp_marques/Marie/.conda/envs/tools/bin/umi_tools
(tools) mkratka@pc-t7-094:/netscratch/dep_mercier/grp_marques/Marie/Luzula_sylvatica/data/scRNA$ /netscratch/dep_mercier/grp_marques/Marie/.conda/envs/tools/bin/umi_tools count

count - Count reads per-gene using UMI and mapping coordinates

Usage: umi_tools count [OPTIONS] --stdin=IN_BAM [--stdout=OUT_BAM]

       note: If --stdout is ommited, standard out is output. To
             generate a valid BAM file on standard out, please
             redirect log with --log=LOGFILE or --log2stderr 

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

Required options missing, see --help for more details

[IanSudbery]

Basically this error will occur whenever the main umi_tools wrapper fails to be able to import one of the subtasks. The error handling code assumes it can't import the required module because it doesn't exist, but in fact it can also occur if the module does exist, but throws an ImportError when imported, which also happens if one of the dependencies is not correctly installed.