Error with installation
Gonzalo Ferreira
(picrust2) manager@bl8vbox[picrust2-2.5.2] pytest [ 3:39AM]
============================= test session starts ==============================
platform linux -- Python 3.8.16, pytest-7.3.1, pluggy-1.0.0
rootdir: /home/manager/Desktop/picrust2-2.5.2
plugins: cov-4.0.0
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', '/home/manager/Desktop/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre...l', '/home/manager/Desktop/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 /home/manager/Desktop/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o /tmp/tmpboytnokt/query_align.stockholm /home/manager/Desktop/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm /home/manager/Desktop/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 /home/manager/Desktop/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/manager/Desktop/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpboytnokt/sepp_out -seed 297834 --alignment /home/manager/Desktop/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpboytnokt/study_seqs_filtered.fasta
Error running this command:
run_sepp.py --tree /home/manager/Desktop/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/manager/Desktop/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpboytnokt/sepp_out -seed 297834 --alignment /home/manager/Desktop/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpboytnokt/study_seqs_filtered.fasta
Standard error of the above failed command:
Traceback (most recent call last):
File "/home/manager/miniconda3/envs/picrust2/bin/run_sepp.py", line 3, in <module>
from sepp.exhaustive import ExhaustiveAlgorithm
File "/home/manager/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/exhaustive.py", line 6, in <module>
from sepp.algorithm import AbstractAlgorithm
File "/home/manager/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/algorithm.py", line 11, in <module>
from sepp.tree import PhylogeneticTree
File "/home/manager/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/tree.py", line 25, in <module>
from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \
ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/home/manager/miniconda3/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 106.33s (0:01:46) ===================
Jörn Horst Bethke Riegel
Hola Gonzalo estoy empezando a utilizar Picrust2 y cuando corro el pytest para ver si quedó correctamente instalado me aparece el mismo error de place_seqs. Encontraste algiuna solucion, me puedes guiar a como corregir el error.
