Test failed

[Former user]

Hi,

I got the following error message after running the ResFinder test using the command: I have installed KMA only ( I don't need BLAST)

python3 tests/functional_tests.py -db_res ./db_resfinder -k ./cge/kma

Can anyone help me with that, thanks in advance

EEEE

ERROR: test_on_data_with_just_acquired_resgene_using_blast (main.ResFinderRunTest)

Traceback (most recent call last): File "tests/functional_tests.py", line 95, in test_on_data_with_just_acquired_resgene_using_blast check=True) File "/home/scotti/miniconda3/lib/python3.7/subprocess.py", line 487, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command 'python3 /mnt/c/Users/scotti/Resfinder_4/resfinder/run_resfinder.py -ifa data/test_isolate_01.fa -o running_test/test1 -s 'Escherichia coli' --min_cov 0.6 -t 0.8 --acquired --db_path_res /mnt/c/Users/scotti/Resfinder_4/resfinder/db_resfinder --blastPath /mnt/c/Users/scotti/Resfinder_4/resfinder/cge/blastn' returned non-zero exit status 1.

====================================================================== ERROR: test_on_data_with_just_acquired_resgene_using_kma (main.ResFinderRunTest)

---

Traceback (most recent call last): File "tests/functional_tests.py", line 153, in test_on_data_with_just_acquired_resgene_using_kma check=True) File "/home/scotti/miniconda3/lib/python3.7/subprocess.py", line 487, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command 'python3 /mnt/c/Users/scotti/Resfinder_4/resfinder/run_resfinder.py -ifq data/test_isolate_01_1.fq data/test_isolate_01_2.fq -o running_test/test2 -s 'Escherichia coli' --min_cov 0.6 -t 0.8 --acquired --db_path_res /mnt/c/Users/scotti/Resfinder_4/resfinder/db_resfinder --kmaPath /mnt/c/Users/scotti/Resfinder_4/resfinder/cge/kma' returned non-zero exit status 1.

====================================================================== ERROR: test_on_data_with_just_point_mut_using_blast (main.ResFinderRunTest)

---

Traceback (most recent call last): File "tests/functional_tests.py", line 210, in test_on_data_with_just_point_mut_using_blast check=True) File "/home/scotti/miniconda3/lib/python3.7/subprocess.py", line 487, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command 'python3 /mnt/c/Users/scotti/Resfinder_4/resfinder/run_resfinder.py -ifa data/test_isolate_05.fa -o running_test/test3 -s 'Escherichia coli' --min_cov 0.6 --threshold 0.8 --point --db_path_point /mnt/c/Users/scotti/Resfinder_4/resfinder/db_pointfinder --blastPath /mnt/c/Users/scotti/Resfinder_4/resfinder/cge/blastn' returned non-zero exit status 1.

====================================================================== ERROR: test_on_data_with_just_point_mut_using_kma (main.ResFinderRunTest)

---

Traceback (most recent call last): File "tests/functional_tests.py", line 253, in test_on_data_with_just_point_mut_using_kma check=True) File "/home/scotti/miniconda3/lib/python3.7/subprocess.py", line 487, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command 'python3 /mnt/c/Users/scotti/Resfinder_4/resfinder/run_resfinder.py -ifq data/test_isolate_05_1.fq data/test_isolate_05_2.fq -o running_test/test4 -s 'Escherichia coli' --min_cov 0.6 --threshold 0.8 --point --db_path_point /mnt/c/Users/scotti/Resfinder_4/resfinder/db_pointfinder --kmaPath /mnt/c/Users/scotti/Resfinder_4/resfinder/cge/kma' returned non-zero exit status 1.

---

Ran 4 tests in 9.378s

FAILED (errors=4)

[Sofie Theisen Honoré]

Dear user.

Thank you for your question! We've just created a new version of ResFinder (4.0) and have been experiencing a bit of problems in that regard. They should however be fixed now. Would you mind trying again? And then of course don't hesitate to write us if you're still having problems!

Best,
Sofie, CGE Helpdesk

[Riccardo]

Hi Sofie,

Thanks for your reply.

I have reinstalled ResFinder and then retested it, but I still get the same error message.

Thanks in advance for your support

Riccardo

‌

‌

EEEE

ERROR: test_on_data_with_just_acquired_resgene_using_blast (main.ResFinderRunTest)

Traceback (most recent call last):
File "tests/functional_tests.py", line 95, in test_on_data_with_just_acquired_resgene_using_blast
check=True)
File "/home/scotti/miniconda3/lib/python3.7/subprocess.py", line 487, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'python3 /mnt/c/Users/scotti/Resfinder_4/resfinder/run_resfinder.py -ifa data/test_isolate_01.fa -o running_test/test1 -s 'Escherichia coli' --min_cov 0.6 -t 0.8 --acquired --db_path_res /mnt/c/Users/scotti/Resfinder_4/resfinder/db_resfinder --blastPath /mnt/c/Users/scotti/Resfinder_4/resfinder/cge/blastn' returned non-zero exit status 1.

======================================================================

ERROR: test_on_data_with_just_acquired_resgene_using_kma (main.ResFinderRunTest)

Traceback (most recent call last):
File "tests/functional_tests.py", line 153, in test_on_data_with_just_acquired_resgene_using_kma
check=True)
File "/home/scotti/miniconda3/lib/python3.7/subprocess.py", line 487, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'python3 /mnt/c/Users/scotti/Resfinder_4/resfinder/run_resfinder.py -ifq data/test_isolate_01_1.fq data/test_isolate_01_2.fq -o running_test/test2 -s 'Escherichia coli' --min_cov 0.6 -t 0.8 --acquired --db_path_res /mnt/c/Users/scotti/Resfinder_4/resfinder/db_resfinder --kmaPath /mnt/c/Users/scotti/Resfinder_4/resfinder/cge/kma' returned non-zero exit status 1.

======================================================================

ERROR: test_on_data_with_just_point_mut_using_blast (main.ResFinderRunTest)

Traceback (most recent call last):
File "tests/functional_tests.py", line 210, in test_on_data_with_just_point_mut_using_blast
check=True)
File "/home/scotti/miniconda3/lib/python3.7/subprocess.py", line 487, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'python3 /mnt/c/Users/scotti/Resfinder_4/resfinder/run_resfinder.py -ifa data/test_isolate_05.fa -o running_test/test3 -s 'Escherichia coli' --min_cov 0.6 --threshold 0.8 --point --db_path_point /mnt/c/Users/scotti/Resfinder_4/resfinder/db_pointfinder --blastPath /mnt/c/Users/scotti/Resfinder_4/resfinder/cge/blastn' returned non-zero exit status 1.

======================================================================

ERROR: test_on_data_with_just_point_mut_using_kma (main.ResFinderRunTest)

Traceback (most recent call last):
File "tests/functional_tests.py", line 253, in test_on_data_with_just_point_mut_using_kma
check=True)
File "/home/scotti/miniconda3/lib/python3.7/subprocess.py", line 487, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'python3 /mnt/c/Users/scotti/Resfinder_4/resfinder/run_resfinder.py -ifq data/test_isolate_05_1.fq data/test_isolate_05_2.fq -o running_test/test4 -s 'Escherichia coli' --min_cov 0.6 --threshold 0.8 --point --db_path_point /mnt/c/Users/scotti/Resfinder_4/resfinder/db_pointfinder --kmaPath /mnt/c/Users/scotti/Resfinder_4/resfinder/cge/kma' returned non-zero exit status 1.

---

Ran 4 tests in 8.170s

FAILED (errors=4)

[Riccardo]

At this stage, I cannot analyse Oxford Nanopore sequencing reads with ResFider, right? Is there any plan to implement it for ONT sequencing reads?

Thanks

[Sofie Theisen Honoré]

Dear Riccardo.
Thank you for your response.
The two blast tests (nr 1 and 3) are supposed to fail because you haven’t installed blast.
The kma test with point mutations (nr 4) might fail because you haven’t provided the path to the pointfinder database. You need to install this, index it and provide the path when running the test script (see instructions in the README of ResFinder).
Will you please try this and get back to me with the result? When I run it on my own computer, test 2 works when I have provided paths to both ResFinder db and PointFinder db - so installing PointFinder might solve both problems.

And no, you can unfortunately not analyse Oxford Nanopore reads with ResFinder. You can see all possible file formats here: https://cge.cbs.dtu.dk/services/resfinder/instructions.php
And no, as far as I know, there is unfortunately no plan to implement it - but I’ll pass it on that there is an interest for it.

Best,
Sofie, CGE Helpdesk