Test Error with BLAST

[Alvin Han]

Hello, I have been trying to install the ResFinder software, and have managed to get the KMA/pointfinder part of the software working, but am having trouble with the blast/acquired resistance gene finder part. When I run the test, it throws an error for the blast tests. The directory containing blastn (/scg/apps/legacy/software/blast/2.2.31+/bin) is in my path, but the test throws errors. Even when I supply the full path to blastn (below), it still throws the same errors. Any help or insight would be great!

Thanks in advance,

Alvin

python3 tests/functional_tests.py -k /oak/stanford/scg/lab_asbhatt/alvinhan/tools/resfinder/cge/kma/kma -b /scg/apps/legacy/software/blast/2.2.31+/bin/blastn
E.E.

ERROR: test_on_data_with_just_acquired_resgene_using_blast (main.ResFinderRunTest)

Traceback (most recent call last):
File "tests/functional_tests.py", line 94, in test_on_data_with_just_acquired_resgene_using_blast
check=True)
File "/usr/lib64/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'python3 /oak/stanford/scg/lab_asbhatt/alvinhan/tools/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 /oak/stanford/scg/lab_asbhatt/alvinhan/tools/resfinder/db_resfinder --blastPath /scg/apps/legacy/software/blast/2.2.31+/bin/blastn' 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 "/usr/lib64/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'python3 /oak/stanford/scg/lab_asbhatt/alvinhan/tools/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 /oak/stanford/scg/lab_asbhatt/alvinhan/tools/resfinder/db_pointfinder --db_path_res /oak/stanford/scg/lab_asbhatt/alvinhan/tools/resfinder/db_resfinder --blastPath /scg/apps/legacy/software/blast/2.2.31+/bin/blastn' returned non-zero exit status 1.

---

Ran 4 tests in 11.924s

FAILED (errors=2)

[Alfred Ferrer Florensa]

Hello Alvin,

I am not sure why the error, as I can run the tests, but we can try to figure it out. It seems the blastn part is failing. Could you try to update the blast version? I am using the version 2.8.1. If then it works, please tell us, and we will state that it is required that version for the ResFinder software.

‌

Best,

Alfred

[CGE Helpdesk]

Dear User,

Did the above suggestion solve your problem, and can we mark the issue as resolved?

Kind regards

Malene, CGE Helpdesk