Hi,
I have encountered some difficulties when installing the latest HUMAnN3 through Conda (humann3 – The Huttenhower Lab), can I get some help solving it? Thank you in advance.
It looks like Minpath and Xipe were not properly installed. If so, how can I manually add the package to the installation? If not, how could this problem be solved?
The detailed code I used for installation and the error msgs are shown below:
code：
(base) [sl24a@ghpcc06 ~]$ bsub -Is -q interactive -app RHEL7 -R rusage[mem=4096] -W 4:00 /bin/bash
Singularity> module load glibc/2.23
Singularity> module load glpk/4.65
Singularity> cp /share/pkg/condas/2018-05-11/condarc_example ~/.condarc
Singularity> conda create --name human python=3.7
Singularity> conda activate human
(human) Singularity> conda config --add channels defaults
(human) Singularity> conda config --add channels bioconda
(human) Singularity> conda config --add channels conda-forge
(human) Singularity> conda config --add channels biobakery
(human) Singularity> conda install humann -c biobakery
Singularity> humann_test
Error message returned from human_test:
======================================================================
ERROR: test_pathways_abundance_with_names (advanced_tests_quantify_modules.TestHumannQuantifyModulesFunctions)
Test the pathways abundance computation (xipe and minpath are off)
Traceback (most recent call last):
File “/home/sl24a/.local/lib/python3.8/site-packages/humann/tests/advanced_tests_quantify_modules.py”, line 634, in test_pathways_abundance_with_names
reactions_database=store.ReactionsDatabase(config.pathways_database_part1)
File “/home/sl24a/.local/lib/python3.8/site-packages/humann/store.py”, line 890, in init
readlines = [line.decode(‘utf-8’) for line in file_handle.readlines()]
File “/share/pkg/condas/2018-05-11/envs/python3.8/lib/python3.8/bz2.py”, line 234, in readlines
return self._buffer.readlines(size)
File “/share/pkg/condas/2018-05-11/envs/python3.8/lib/python3.8/_compression.py”, line 68, in readinto
data = self.read(len(byte_view))
File “/share/pkg/condas/2018-05-11/envs/python3.8/lib/python3.8/_compression.py”, line 99, in read
raise EOFError("Compressed file ended before the "
EOFError: Compressed file ended before the end-of-stream marker was reached
======================================================================
ERROR: test_pathways_coverage_with_names (advanced_tests_quantify_modules.TestHumannQuantifyModulesFunctions)
Test the pathways coverage computation (xipe and minpath are off)
Traceback (most recent call last):
File “/home/sl24a/.local/lib/python3.8/site-packages/humann/tests/advanced_tests_quantify_modules.py”, line 580, in test_pathways_coverage_with_names
reactions_database=store.ReactionsDatabase(config.pathways_database_part1)
File “/home/sl24a/.local/lib/python3.8/site-packages/humann/store.py”, line 890, in init
readlines = [line.decode(‘utf-8’) for line in file_handle.readlines()]
File “/share/pkg/condas/2018-05-11/envs/python3.8/lib/python3.8/bz2.py”, line 234, in readlines
return self._buffer.readlines(size)
File “/share/pkg/condas/2018-05-11/envs/python3.8/lib/python3.8/_compression.py”, line 68, in readinto
data = self.read(len(byte_view))
File “/share/pkg/condas/2018-05-11/envs/python3.8/lib/python3.8/_compression.py”, line 99, in read
raise EOFError("Compressed file ended before the "
EOFError: Compressed file ended before the end-of-stream marker was reached
Ran 186 tests in 9.940s
FAILED (errors=2)