long non regression tests

Failed Started 2 weeks ago by
1Running with gitlab-runner 17.1.1 (21127735)
2  on k8sprod-02 qTP56ycQz, system ID: r_Pem8oLs0fone
 3  Preparing the "kubernetes" executor  
  00:00
4Using Kubernetes namespace: gitlab-ci
5Using Kubernetes executor with image registry-gitlab.pasteur.fr/dsi-tools/docker-images:redhat_ptv ...
6Using attach strategy to execute scripts...
 7  Preparing environment  
  00:04
8Using FF_USE_POD_ACTIVE_DEADLINE_SECONDS, the Pod activeDeadlineSeconds will be set to the job timeout: 60h0m0s...
9Waiting for pod gitlab-ci/runner-qtp56ycqz-project-1263-concurrent-1-9zlkhxr6 to be running, status is Pending
10Running on runner-qtp56ycqz-project-1263-concurrent-1-9zlkhxr6 via gitlab-runner-56654dd868-t29fq...
 11  Getting source from Git repository  
  01:09
12Fetching changes...
13Initialized empty Git repository in /builds/vlegrand/ptv/.git/
14Created fresh repository.
15Checking out 9edd1e8b as detached HEAD (ref is master)...
16Skipping Git submodules setup
 17  Executing "step_script" stage of the job script  
  00:16
18$ export SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True
19$ poetry install
20Creating virtualenv phagetermvirome-1Plpl7Bq-py3.9 in /root/.cache/pypoetry/virtualenvs
21Installing dependencies from lock file
22Package operations: 23 installs, 0 updates, 0 removals
23  • Installing six (1.16.0)
24  • Installing numpy (1.25.2)
25  • Installing python-dateutil (2.8.2)
26  • Installing pytz (2023.3)
27  • Installing tzdata (2023.3)
28  • Installing zipp (3.16.2)
29  • Installing contourpy (1.1.0)
30  • Installing cycler (0.11.0)
31  • Installing fonttools (4.42.1)
32  • Installing importlib-resources (6.0.1)
33  • Installing joblib (1.3.2)
34  • Installing kiwisolver (1.4.5)
35  • Installing packaging (23.1)
36  • Installing pandas (2.1.0)
37  • Installing patsy (0.5.3)
38  • Installing pillow (10.0.0)
39  • Installing pyparsing (3.0.9)
40  • Installing scipy (1.11.2)
41  • Installing threadpoolctl (3.2.0)
42Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
43Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
44Connection pool is full, discarding connection: pypi.org. Connection pool size: 10
45  • Installing matplotlib (3.7.2)
46  • Installing reportlab (4.0.4)
47  • Installing statsmodels (0.14.0)
48  • Installing scikit-learn (1.3.0)
49Installing the current project: phagetermvirome (4.3)
50$ source `poetry env info --path`/bin/activate
51$ export PYTHONPATH=$PYTHONPATH:./phagetermvirome
52$ cd non-regression-tests
53$ bash run_HK97_long.sh
54running PhageTerm on HK97 genome and a dataset with a minimum 50x coverage
55running nrt tests
56Traceback (most recent call last):
57  File "/builds/vlegrand/ptv/non-regression-tests/../phagetermvirome/PhageTerm.py", line 295, in <module>
58    main()
59  File "/builds/vlegrand/ptv/non-regression-tests/../phagetermvirome/PhageTerm.py", line 57, in main
60    inRawDArgs, fParms, tParms, inDArgs=checkOptArgsConsistency(getopt)
61  File "/builds/vlegrand/ptv/phagetermvirome/main_utils.py", line 483, in checkOptArgsConsistency
62    inRawDArgs = inputRawDataArgs(options.fastq, options.reference, options.host, options.analysis_name, options.paired,
63  File "/builds/vlegrand/ptv/phagetermvirome/main_utils.py", line 241, in __init__
64    self.tot_reads = totReads(fastq)
65  File "/builds/vlegrand/ptv/phagetermvirome/IData_handling.py", line 297, in totReads
66    for l in buffered_f:
67AttributeError: '_io.TextIOWrapper' object has no attribute 'readinto'
 68  Cleaning up project directory and file based variables  
  00:01
69ERROR: Job failed: command terminated with exit code 1