Error in calculate_dirichlet_abundances.py. - ValueError: could not convert string to float

[BenjaminGuinet]

Hello while running haystac --mode abundances on my data I got this following snakemake error :

Error in rule calculate_dirichlet_abundances:
    jobid: 0
    output: /crex/proj/snic2022-6-144/nobackup/user/Meta_project/Virus/Haystac_analysis/Scripts/Herpesvirus_sequences/L010_Herpesvirus_db_output/probabilities/L010/L010_posterior_abundance.tsv
    log: /crex/proj/snic2022-6-144/nobackup/user/Meta_project/Virus/Haystac_analysis/Scripts/Herpesvirus_sequences/L010_Herpesvirus_db_output/probabilities/L010/L010_posterior_abundance.log (check log file(s) for error message)
    conda-env: /home/user/haystac/cache/conda/3983e9d32a119d531dde75cf1fd7d0a0

RuleException:
CalledProcessError in line 169 of /home/user/.conda/envs/haystac/lib/python3.6/site-packages/haystac/workflow/rules/metagenomics.smk:
Command 'source /sw/apps/conda/latest/rackham_stage/bin/activate '/home/user/haystac/cache/conda/3983e9d32a119d531dde75cf1fd7d0a0'; set -euo pipefail;  python /crex/proj/snic2022-6-144/nobackup/user/Meta_project/Virus/Haystac_analysis/Scripts/Herpesvirus_sequences/.snakemake/scripts/tmpjizpoz5a.calculate_dirichlet_abundances.py' returned non-zero exit status 1.
  File "/home/user/.conda/envs/haystac/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 2352, in run_wrapper
  File "/home/user/.conda/envs/haystac/lib/python3.6/site-packages/haystac/workflow/rules/metagenomics.smk", line 169, in __rule_calculate_dirichlet_abundances
  File "/home/user/.conda/envs/haystac/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 569, in _callback
  File "/home/user/.conda/envs/haystac/lib/python3.6/concurrent/futures/thread.py", line 56, in run
  File "/home/user/.conda/envs/haystac/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 555, in cached_or_run
  File "/home/user/.conda/envs/haystac/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 2364, in run_wrapper
Trying to restart job 0.`

And when looking at the log file I see :

144/nobackup/user/Meta_project/Virus/Haystac_analysis/Scripts/Herpesvirus_sequences/L010_Herpesvirus_db_output/probabilities/L010/L010_posterior_abundance.log
Traceback (most recent call last):
  File "/crex/proj/snic2022-6-144/nobackup/user/Meta_project/Virus/Haystac_analysis/Scripts/Herpesvirus_sequences/.snakemake/scripts/tmp5j1s7h8q.calculate_dirichlet_abu
ndances.py", line 145, in <module>
    calculate_dirichlet_abundances(
  File "/crex/proj/snic2022-6-144/nobackup/user/Meta_project/Virus/Haystac_analysis/Scripts/Herpesvirus_sequences/.snakemake/scripts/tmp5j1s7h8q.calculate_dirichlet_abu
ndances.py", line 84, in calculate_dirichlet_abundances
    a = ts_tv_matrix.groupby("Taxon").sum().squeeze().astype(float)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.local/lib/python3.11/site-packages/pandas/core/generic.py", line 6324, in astype
    new_data = self._mgr.astype(dtype=dtype, copy=copy, errors=errors)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.local/lib/python3.11/site-packages/pandas/core/internals/managers.py", line 451, in astype
    return self.apply(
           ^^^^^^^^^^^
  File "/home/user/.local/lib/python3.11/site-packages/pandas/core/internals/managers.py", line 352, in apply
    applied = getattr(b, f)(**kwargs)
              ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.local/lib/python3.11/site-packages/pandas/core/internals/blocks.py", line 511, in astype
    new_values = astype_array_safe(values, dtype, copy=copy, errors=errors)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.local/lib/python3.11/site-packages/pandas/core/dtypes/astype.py", line 242, in astype_array_safe
    new_values = astype_array(values, dtype, copy=copy)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.local/lib/python3.11/site-packages/pandas/core/dtypes/astype.py", line 187, in astype_array
    values = _astype_nansafe(values, dtype, copy=copy)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.local/lib/python3.11/site-packages/pandas/core/dtypes/astype.py", line 138, in _astype_nansafe
    return arr.astype(dtype, copy=True)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: could not convert string to float: 'ERR5024913.26762701ERR5024914.36341165ERR5024913.39738624ERR5024914.9765425ERR5024914.48021130ERR5024913.12985897ERR5024913.17020599

So I looked into the haystac code and

On line 78 in the code of calculate_dirichlet_abundances.py I found this :

if len(ts_tv_matrix.Taxon.unique()) > 1:
    a = ts_tv_matrix.groupby("Taxon").sum().squeeze().astype(float)
else:
    a = ts_tv_matrix.groupby("Taxon").sum().iloc[:, 0].astype(float)
a.loc["Grey_Matter"] = grey_matter.sum()

It looks like that it is this part that gives this error : ValueError: could not convert string to float: 'ERR5024913.26762701ERR5024914.36341165ERR5024913.39738624ERR5024914.9765425ERR5024914.48021130ERR5024913.12985897ERR5024913.17020599

Because the ts_tv_matrix at this step looks like that :

                                    Taxon              Read_ID  Dirichlet_Assignment
0     Columbid_alphaherpesvirus_1_strain_HLJ  ERR5024913.47906133                   0.0
1     Columbid_alphaherpesvirus_1_strain_HLJ  ERR5024913.16245378                   0.0
2     Columbid_alphaherpesvirus_1_strain_HLJ   ERR5024913.5227225                   0.0
3     Columbid_alphaherpesvirus_1_strain_HLJ   ERR5024913.2444664                   0.0
4     Columbid_alphaherpesvirus_1_strain_HLJ  ERR5024913.13611153                   0.0
...                                      ...                  ...                   ...
1942         Human_herpesvirus_2_strain_HG52  ERR5024914.75275187                   0.0
1943         Human_herpesvirus_2_strain_HG52  ERR5024913.36437085                   0.0
1944         Human_herpesvirus_2_strain_HG52  ERR5024914.41555325                   0.0
1945         Human_herpesvirus_2_strain_HG52  ERR5024913.40749291                   0.0
1946         Human_herpesvirus_2_strain_HG52  ERR5024913.66974822                   0.0

So it looks like my tsv files does look like has it should our did I missed something ? Thanks for your help.

Here is the full haystac code I used : haystac analyse --mode abundances --database Herpesvirus_db --sample L010 --output L010_Herpesvirus_db_output --cores 15

[antonisdim]

Hello Benjamin,

I hope you are doing great, and apologies for not getting back to you earlier !

You are right in terms of which line is causing that ValueError to be raised, and your ts_tv_matrix also looks fine.

I have been trying to reproduce your error locally, using the the example snippet of your ts_tv_matrix. I have managed to reproduce your error only when I use a version of pandas higher than the one that is specified in the yaml file used to create the /home/user/haystac/cache/conda/3983e9d32a119d531dde75cf1fd7d0a0 conda env. In that yaml file the pandas version is specified to be 1.0.3, and it appears you might be using a version that is >= 1.4.1. Which makes sense as your python version within that env also changes to python3.11. Unfortunately I am not sure how this happened as whenever I am creating that env locally, it gets built correctly.

I think if you downgrade your pandas, or build that env with the correct dependency versions (as pinned in the envs/scipy.yaml), your analysis should work.

That being said, thank you for raising this issue ! It's a good reason to update the versions of some dependencies, which I will get round to doing soon.

Please let me know if this helps !

Best, Antony