LooseVersion' object has no attribute 'version

[mabouelk]

Any help!

Running ariba prepareref with:
/Users/mohamedabouelkhair/miniconda3/envs/ariba/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF

Traceback (most recent call last):
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/bin/ariba", line 312, in
args.func(args)
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.6/site-packages/ariba/tasks/prepareref.py", line 9, in run
extern_progs, version_report_lines = versions.get_all_versions(using_spades=False)
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.6/site-packages/ariba/versions.py", line 21, in get_all_versions
extern_progs = external_progs.ExternalProgs(fail_on_error=False, using_spades=using_spades)
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.6/site-packages/ariba/external_progs.py", line 88, in init
if prog in min_versions and LooseVersion(version) < LooseVersion(min_versions[prog]):
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.6/distutils/version.py", line 52, in lt
c = self._cmp(other)
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.6/distutils/version.py", line 335, in _cmp
if self.version == other.version:
AttributeError: 'LooseVersion' object has no attribute 'version'

Something went wrong. See above for error message(s). Return code was 1

[markb729]

I encountered this too, which may be related to an error manifested in the bioconda version and/or an unknown "feature" lurking in the python 3.6 env. My solution was to create a python 3.8.3 env including gcc-4.8.5 (needed for ariba compilation and also includes zlib). Then install the package with pip3 install ariba to work as advertised.

[mabouelk]

Great, it works. Thank you so much

[mabouelk]

when I run

ariba test output

I got the following error, even the files are there. Should I specify the path?

The following reads file(s) were not found:
reads_1.fq
reads_2.fq
Cannot continue
Traceback (most recent call last):
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/bin/ariba", line 312, in
args.func(args)
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.8/site-packages/ariba/tasks/run.py", line 65, in run
c.run()
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.8/site-packages/ariba/clusters.py", line 612, in run
self._run()
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.8/site-packages/ariba/clusters.py", line 637, in _run
self._init_and_run_clusters()
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.8/site-packages/ariba/clusters.py", line 465, in _init_and_run_clusters
manager = multiprocessing.Manager()
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.8/multiprocessing/context.py", line 57, in Manager
m.start()
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.8/multiprocessing/managers.py", line 583, in start
self._address = reader.recv()
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.8/multiprocessing/connection.py", line 250, in recv
buf = self._recv_bytes()
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.8/multiprocessing/connection.py", line 414, in _recv_bytes
buf = self._recv(4)
File "/Users/mohamedabouelkhair/miniconda3/envs/ariba/lib/python3.8/multiprocessing/connection.py", line 383, in _recv
raise EOFError
EOFError

Something went wrong. See above for error message(s). Return code was 1

[markb729]

Paths are self-contained within the test and do not require specification. Nevertheless, try running ariba test output within the ariba directory. It should first prepare the input data:

Made output directory output. Copying test data files into it:

copied ref_seqs.fa
copied metadata.tsv
copied reads_1.fq
copied reads_2.fq

and then follow with prepareref:

Running ariba prepareref with:

/mnt/software/anaconda/envs/ariba_test/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF

It will also output paths to external dependencies, including python packages. Pay attention to these and ariba will fail if any are absent.

ariba   2.14.5  /mnt/software/anaconda/envs/ariba_test/lib/python3.8/site-packages/ariba/__init__.py
bs4     4.9.1   /mnt/software/anaconda/envs/ariba_test/lib/python3.8/site-packages/bs4/__init__.py
dendropy        4.4.0   /mnt/software/anaconda/envs/ariba_test/lib/python3.8/site-packages/dendropy/__init__.py
pyfastaq        3.17.0  /mnt/software/anaconda/envs/ariba_test/lib/python3.8/site-packages/pyfastaq/__init__.py
pymummer        0.10.3  /mnt/software/anaconda/envs/ariba_test/lib/python3.8/site-packages/pymummer/__init__.py
pysam   0.16.0.1        /mnt/software/anaconda/envs/ariba_test/lib/python3.8/site-packages/pysam/__init__.py

Clearly the test is not completing input data preparation. If you run the test within the ariba folder and still get the error, then this is most likely a conda environment issue. I would recommend starting by updating your conda package and/or starting from a clean environment.

[rpetit3]

Hi @mabouelk

I'm a bit late to the party but the error (AttributeError: 'LooseVersion' object has no attribute 'version') was due to the latest Bowtie2 version Bioconda not outputting the version number.

Here are some related issues:

BenLangmead/bowtie2#301

bioconda/bioconda-recipes#22836

I've submitted a PR to Bioconda to pin the Bowtie2 version to <2.4 which should fix things for you.

Cheers!