Results Problem

[Former user]

Hello, I followed all steps except the BLAST part, however I'm using FASTQ. When I try to run I get this message: PS C:\Users\diogo\Desktop\Resfinder\resfinder> python3 run_resfinder.py -o C:/Users/diogo/Desktop/ResFinder/Results -s "Other" -l 0.6 -t 0.8 --acquired -ifq E:/SRR7631476_1.fastq -k C:/Users/diogo/Desktop/ResFinder/resfinder/cge/kma -db_res C:/Users/diogo/Desktop/ResFinder/resfinder/db_resfinder -db_point C:/Users/diogo/Desktop/ResFinder/resfinder/db_pointfinder Traceback (most recent call last): File "C:\Users\diogo\Desktop\Resfinder\resfinder\run_resfinder.py", line 228, in <module> _ = subprocess.check_output([kma, "-h"]) File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 424, in check_output
return run(popenargs, stdout=PIPE, timeout=timeout, check=True, File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 505, in run with Popen(popenargs, **kwargs) as process: File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 951, in init
self._execute_child(args, executable, preexec_fn, close_fds, File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 1420, in _execute_child hp, ht, pid, tid = _winapi.CreateProcess(executable, args, PermissionError: [WinError 5] Acesso negado

[CGE Helpdesk]

Dear Mr/Ms,

Thank you for the interest in our services and for reporting your issue.

It looks like it fails when trying to run subprocess.check_output([kma, "-h"]), and the issue might have something to do with the installation of kma. How did you install kma?

And did you install the ResFinder database with kma with the following commands:?

cd path/to/db_resfinder
python3 INSTALL.py

If yes, could you kindly check the contents of the ResFinder database, and make sure that a lot of new files has appeared, e.g. with file endings .length.b, .comp.b etc., apart from just the .fsa files.

If these files are present, and it still doesn’t work, kindly try to run the job on our webserver if possible: https://cge.cbs.dtu.dk/services/ResFinder/ It is likely, that the job doesn’t fail, but this way we can see if the problem is local or not. And please pass the URL for the job to our helpdesk: [e-mail] .

Kind regards

Malene, CGE Helpdesk

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