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jodyphelan / TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
GNU General Public License v3.0
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v6.2.0 fails to import tbdb (whov2) #339

Closed abhi18av closed 2 months ago

abhi18av commented 3 months ago

Hi @jodyphelan ,

I noticed that there was a bugfix in v6.2.0 and I tested this release regarding the use of WHOv2 directly.

The problem seems to be stemming from the pathogenprofiler dependency 🤔

For some reason, the v6.0.0 works fine on conda ✅ and biocontainer ✅ 


~ 🅒 tb-profiler-env
+  p$ tb-profiler --version
tb-profiler version 6.0.0

+  p$ tb-profiler update_tbdb --commit 22e9ceb6433d02071222af8dca506c6348604877 --logging DEBUG
[13:53:26] DEBUG    Running command: git clone https://github.com/jodyphelan/tbdb.git                                        utils.py:489
[13:53:28] DEBUG    Running command: git checkout master                                                                     utils.py:489
[13:53:29] DEBUG    Running command: git pull                                                                                utils.py:489
           DEBUG    Running command: git checkout 22e9ceb6433d02071222af8dca506c6348604877                                   utils.py:489
           DEBUG    Running command: tb-profiler create_db --prefix tbdb --csv mutations.csv --watchlist watchlist.csv       utils.py:489
                    --rules rules.txt --load
[13:53:30] DEBUG    Removing temporary files: 8198346a-a17c-4f9f-9a61-fdca995076b8                                            utils.py:29
           INFO     Sucessfully updated TBDB                                                                              tb-profiler:218

~ 🅒 tb-profiler-env
+  p$ micromamba install tb-profiler=6.2.0

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

gurobi/noarch                                      130.0 B @ 159.0 B/s  0.9s
gurobi/osx-64                                        4.6kB @   4.6kB/s  1.0s
bioconda/osx-64                                      4.4MB @   3.7MB/s  1.3s
pkgs/r/noarch                                                 No change
pkgs/r/osx-64                                                 No change
bioconda/noarch                                      5.2MB @   2.7MB/s  1.2s
pkgs/main/noarch                                   861.6kB @ 398.7kB/s  0.3s
conda-forge/noarch                                  16.3MB @   7.4MB/s  2.5s
pkgs/main/osx-64                                     6.4MB @   1.6MB/s  2.8s
conda-forge/osx-64                                  34.8MB @   7.3MB/s  5.7s

Pinned packages:
  - python 3.10.*

Transaction

  Prefix: /Users/abhi/.micromamba/envs/tb-profiler-env

  Updating specs:

   - tb-profiler=6.2.0

  Package              Version  Build         Channel             Size
────────────────────────────────────────────────────────────────────────
  Upgrade:
────────────────────────────────────────────────────────────────────────

  - pathogen-profiler    4.0.0  pyh7cba7a3_0  bioconda            57kB
  + pathogen-profiler    4.1.0  pyh7cba7a3_0  bioconda/noarch     57kB
  - tb-profiler          6.0.0  pyhdfd78af_0  bioconda             9MB
  + tb-profiler          6.2.0  pyhdfd78af_0  bioconda/noarch      9MB

  Summary:

  Upgrade: 2 packages

  Total download: 9MB

────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] Y

Transaction starting
pathogen-profiler                                   57.5kB @ 340.0kB/s  0.2s
tb-profiler                                          8.9MB @  13.9MB/s  0.6s
Changing pathogen-profiler-4.0.0-pyh7cba7a3_0 ==> pathogen-profiler-4.1.0-pyh7cba7a3_0
Changing tb-profiler-6.0.0-pyhdfd78af_0 ==> tb-profiler-6.2.0-pyhdfd78af_0

Transaction finished

To activate this environment, use:

    $ [micro]mamba activate <environment>

Or to execute a single command in this environment, use:

    $ [micro]mamba run -n <environment> mycommand

~ 🅒 tb-profiler-env
+  p$ tb-profiler update_tbdb --commit 22e9ceb6433d02071222af8dca506c6348604877 --logging DEBUG
[14:06:50] DEBUG    Running command: git checkout tbdb                                                                       utils.py:480
           DEBUG    Running command: git pull                                                                                utils.py:480
[14:06:51] DEBUG    Running command: git checkout 22e9ceb6433d02071222af8dca506c6348604877                                   utils.py:480
           DEBUG    Running command: tb-profiler create_db --prefix tbdb --csv mutations.csv --watchlist watchlist.csv       utils.py:480
                    --rules rules.txt --load
[14:06:52] ERROR                                                                                                             utils.py:485
           DEBUG    Removing temporary files: 2dff4499-3481-4d9a-94d6-746a4f09a2ed                                            utils.py:32
Traceback (most recent call last):
  File "/Users/abhi/.micromamba/envs/tb-profiler-env/bin/tb-profiler", line 583, in <module>
    args.func(args)
  File "/Users/abhi/.micromamba/envs/tb-profiler-env/bin/tb-profiler", line 211, in main_update_tbdb
    pp.run_cmd(f"tb-profiler create_db --prefix {args.prefix} --csv mutations.csv --watchlist watchlist.csv {extra_args} --load")
  File "/Users/abhi/.micromamba/envs/tb-profiler-env/lib/python3.10/site-packages/pathogenprofiler/utils.py", line 486, in run_cmd
    raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,result.stderr.decode()))
ValueError: Command Failed:
/bin/bash -c set -o pipefail; tb-profiler create_db --prefix tbdb --csv mutations.csv --watchlist watchlist.csv --rules rules.txt --load
stderr:

Cleaning up after failed run
           ERROR                                                                                                           tb-profiler:59

                    ################################# ERROR #######################################

                    This run has failed. Please check all arguments and make sure all input files
                    exist. If no solution is found, please open up an issue at
                    https://github.com/jodyphelan/TBProfiler/issues/new and paste or attach the
                    contents of the error log (tbdb.errlog.txt)

                    ###############################################################################

~ 🅒 tb-profiler-env
+  p$
abhi18av commented 2 months ago

Hi @jodyphelan , could you please let us know when is the next patch release scheduled?

abhi18av commented 2 months ago

Closing this issue as this has been address with https://github.com/jodyphelan/tbdb/commit/bdace1f82d948ce0001e1dade6eb93d2da9c47e5

Thanks Jody!