tests/test_place_seqs.py shows failed status upon running the 'pytest' command

[Christaline-George]

I have installed the latest version of picrust2 (v2.5.2).

While the installation prompted that installation was successful, runnin the pytest command showed the following error:

==================================================================== test session starts ====================================================================
platform linux -- Python 3.8.18, pytest-7.4.3, pluggy-1.3.0
rootdir: /hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2
plugins: cov-4.1.0
collected 61 items

tests/test_hsp.py ........ [ 13%]
tests/test_metagenome_pipeline.py ............... [ 37%]
tests/test_pathway_pipeline.py .... [ 44%]
tests/test_place_seqs.py ........F [ 59%]
tests/test_util.py .................... [ 91%]
tests/test_workflow.py ..... [100%]

========================================================================= FAILURES ==========================================================================
____________________________________________________ place_seqs_tests.test_run_place_seqs_pipeline_sepp _____________________________________________________

self = <tests.test_place_seqs.place_seqs_tests testMethod=test_run_place_seqs_pipeline_sepp>

def test_run_place_seqs_pipeline_sepp(self):
    '''Basic test of full place seqs pipeline with SEPP. Just run to
       see if any errors occur'''
    with TemporaryDirectory() as temp_dir:
        tmp_tree = path.join(temp_dir, "out.tre")

      place_seqs_pipeline(study_fasta=test_study_seqs,

                            ref_dir=default_ref_dir,
                            placement_tool="sepp",
                            out_tree=tmp_tree,
                            threads=1,
                            out_dir=temp_dir,
                            min_align=0.8,
                            chunk_size=5000,
                            verbose=True)

tests/test_place_seqs.py:160:

---

picrust2/place_seqs.py:95: in place_seqs_pipeline
run_sepp(tree=tree,
picrust2/place_seqs.py:458: in run_sepp
system_call_check(sepp_command, print_command=print_cmds,

---

cmd = ['run_sepp.py', '--tree', '/hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro...isg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info', '--cpu', ...]
print_command = True, print_stdout = True, print_stderr = True

def system_call_check(cmd, print_command=False, print_stdout=False,
                      print_stderr=False):
    '''Run system command and throw and error if return is not 0. Input command
    can be a list containing the command or a string.'''

    # Convert command to list if input as string.
    if type(cmd) is str:
        cmd = cmd.split()

    # Print command out if option set.
    if print_command:
        print(" ".join(cmd), file=sys.stderr)

    stdout_log = ""
    stderr_log = ""

    # Write stdout and stderr of command to temporary files.
    # Only output the content of these files if the job fails.
    with TemporaryDirectory() as temp_dir:

        stdout_file = join(temp_dir, "stdout.txt")
        stderr_file = join(temp_dir, "stderr.txt")

        with open(stdout_file, "wb") as stdout_fh, \
             open(stderr_file, "wb") as stderr_fh:

            return_value = call(cmd, stdout=stdout_fh,
                                stderr=stderr_fh)

        # Capture stdout and stderr.
        with open(stdout_file, 'r') as stdout_fh:
            stdout_log = stdout_fh.read()

        with open(stderr_file, 'r') as stderr_fh:
            stderr_log = stderr_fh.read()

        # Exit with error if command did not finish successfully.
        if return_value != 0:
            print("\nError running this command:\n" + " ".join(cmd),
                  file=sys.stderr)

            if stdout_log:
                print("\nStandard output of the above failed command:\n" +
                      stdout_log, file=sys.stderr)

            if stderr_log:
                print("\nStandard error of the above failed command:\n" +
                      stderr_log, file=sys.stderr)

          sys.exit(1)

E SystemExit: 1

picrust2/util.py:258: SystemExit
------------------------------------------------------------------- Captured stdout call --------------------------------------------------------------------

------------------------------------------------------------------- Captured stderr call --------------------------------------------------------------------
hmmalign --trim --dna --mapali /hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o /tmp/tmpcn6ncfol/query_align.stockholm /hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm /hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/tests/test_data/place_seqs/study_seqs_test.fasta

All raw input sequences were the same length (400)

run_sepp.py --tree /hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpcn6ncfol/sepp_out -seed 297834 --alignment /hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpcn6ncfol/study_seqs_filtered.fasta

Error running this command:
run_sepp.py --tree /hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpcn6ncfol/sepp_out -seed 297834 --alignment /hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpcn6ncfol/study_seqs_filtered.fasta

Standard error of the above failed command:
Traceback (most recent call last):
File "/home/svu/chrisg25/TMFZ/postDADA2/picrust2-2.5.2/miniforge3/envs/picrust2/bin/run_sepp.py", line 3, in
from sepp.exhaustive import ExhaustiveAlgorithm
File "/hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/miniforge3/envs/picrust2/lib/python3.8/site-packages/sepp/exhaustive.py", line 6, in
from sepp.algorithm import AbstractAlgorithm
File "/hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/miniforge3/envs/picrust2/lib/python3.8/site-packages/sepp/algorithm.py", line 11, in
from sepp.tree import PhylogeneticTree
File "/hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/miniforge3/envs/picrust2/lib/python3.8/site-packages/sepp/tree.py", line 25, in
from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as
ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/hpctmp/chrisg25/R_out/TMFZ/postDADA2/picrust2-2.5.2/miniforge3/envs/picrust2/lib/python3.8/site-packages/dendropy/datamodel/treemodel/init.py)

================================================================== short test summary info ==================================================================
FAILED tests/test_place_seqs.py::place_seqs_tests::test_run_place_seqs_pipeline_sepp - SystemExit: 1
========================================================= 1 failed, 60 passed in 905.97s (0:15:05) =

[R-Wright-1]

Hi there, how did you install it? Please note that on the installation instructions page , it says "Run the tests to verify the installation (note that this wont work if you followed the bioconda install instructions, unless you also downloaded the source code and navigated to the main directory)"

[ArnaudBelcour]

Hi,

I had the same error, it is an issue with sepp and a version of dendropy (it has been described in this other issue: #312). To solve this, you can use dendropy version 4.5.2 by installing it with pip install dendropy==4.5.2.

[R-Wright-1]

Thanks for this fix @ArnaudBelcour!

[nnthule]

Hello, I am encountering the exact same error when I ran pytest after installing picrust2 2.6.0. I tried the pip install dendropy==4.5.2 but the same error persisted. I currently have sepp version 4.5.5. Do you have any suggestion on how I could fix this?

[Mincana-Huang]

Hi, I had the same problem on picrust2 latest version 2.6.1. I tried force downgrading dendropy to 4.5.2 but the error did not change. Is there any way to solve this problem?

[R-Wright-1]

Hi there,

Could you both give some more details on how you are installing PICRUSt2 and what kind of computer you are working with please? Also the current version of dendropy required is 5.0.2 - you can see all dependencies here.

Robyn

[Mincana-Huang]

Hi there,

Could you both give some more details on how you are installing PICRUSt2 and what kind of computer you are working with please? Also the current version of dendropy required is 5.0.2 - you can see all dependencies here.

Robyn

Hi,

I am new to picrust2. I downloaded picrust2 latest version 2.6.1 and copied the code from picrust2-wiki-Installation to install it:

tar xvzf picrust2-2.6.1.tar.gz
cd picrust2-2.6.1/
mamba env create -f picrust2-env.yaml
conda activate picrust2
pip install --editable .

I saw a previous conversation saying that I needed to use dendropy version 4.5.2. I tried it and found that the problem was not solved.

I use WSL system. I tried using epa-ng method and it worked well.

[R-Wright-1]

I unfortunately don't have any experience using WSL, so am unable to give any specific recommendations there and I also don't know if I would expect this to work in the same way or not. But unless you are unhappy using epa-ng, if using epa-ng worked for you and you were able to run PICRUSt2, then I would say not to worry/spend more time trying to troubleshoot this.

Robyn

[nnthule]

Thank you for your reply, @R-Wright-1 . I also installed picrust2 from source (picrust2-2.6.0.tar.gz) on a WSL system. The thing is, I could not run the epa-ng method due to limited memory (my RAM is only 8 GB), so I hope to try the sepp method. Since you said the current version of dendropy required is 5.0.2, do you think changing to this dendropy version would allow me to use the sepp method? In other words, would the sepp version 4.5.5 I have be compatible with dendropy 5.0.2?

[R-Wright-1]

Hi again,

You could try removing any dendropy version requirement and see if that works, so replace the line - dendropy =5.0.1 with - dendropy. But I don't think that you will need to change the sepp version that you have.

Robyn