bed format error when testing on amplicon & ref on other viruses
Closed this issue · 2 comments
Hi there, thank you for creating this amazing tools !
I recently work on other viruses and try to customize my own primers in bed format, i flagged correctly "_LEFT" and "_RIGHT" to the scheme. But somewhat still getting this error:
Traceback (most recent call last):
File "/home/ihcm-ubuntu/interartic_bin/lib/python3.7/site-packages/flask/app.py", line 2464, in call
return self.wsgi_app(environ, start_response)
File "/home/ihcm-ubuntu/interartic_bin/lib/python3.7/site-packages/flask/app.py", line 2450, in wsgi_app
response = self.handle_exception(e)
File "/home/ihcm-ubuntu/interartic_bin/lib/python3.7/site-packages/flask/app.py", line 1867, in handle_exception
reraise(exc_type, exc_value, tb)
File "/home/ihcm-ubuntu/interartic_bin/lib/python3.7/site-packages/flask/_compat.py", line 39, in reraise
raise value
File "/home/ihcm-ubuntu/interartic_bin/lib/python3.7/site-packages/flask/app.py", line 2447, in wsgi_app
response = self.full_dispatch_request()
File "/home/ihcm-ubuntu/interartic_bin/lib/python3.7/site-packages/flask/app.py", line 1952, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/home/ihcm-ubuntu/interartic_bin/lib/python3.7/site-packages/flask/app.py", line 1821, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/home/ihcm-ubuntu/interartic_bin/lib/python3.7/site-packages/flask/_compat.py", line 39, in reraise
raise value
File "/home/ihcm-ubuntu/interartic_bin/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request
rv = self.dispatch_request()
File "/home/ihcm-ubuntu/interartic_bin/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request
return self.view_functionsrule.endpoint
File "/home/ihcm-ubuntu/interartic_bin/main.py", line 940, in parameters
new_job = qSys.newJob(job_name, input_folder, read_file, primer_scheme_dir, primer_scheme, primer_type, output_folder, normalise, num_threads, pipeline, min_length, max_length, bwa, skip_nanopolish, dry_run, override_data, num_samples, guppyplex, barcode_type, input_name, csv_filepath, primer_select, input_name)
File "/home/ihcm-ubuntu/interartic_bin/src/system.py", line 25, in newJob
return Job(job_name, input_folder, read_file, primer_scheme_dir, primer_scheme, primer_type, output_folder, normalise, num_threads, pipeline, min_length, max_length, bwa, skip_nanopolish, dry_run, override_data, num_samples, guppyplex, barcode_type, run_name, csv_file, primer_select, input_name)
File "/home/ihcm-ubuntu/interartic_bin/src/job.py", line 42, in init
self._plot_cmd = self.__generatePlotCmd()
File "/home/ihcm-ubuntu/interartic_bin/src/job.py", line 520, in __generatePlotCmd
plot_cmd = plot_cmd + "; covarPlots.py -v {} -d1 {} -d2 {} -b {}".format(vcf_file, depth1, depth2, bed_file) + " >> " + self._output_folder + "/all_cmds_log.txt 2>>" + self._output_folder + "/all_cmds_log.txt"
UnboundLocalError: local variable 'bed_file' referenced before assignment
Is anyone know what error could i have committed?
issue solved: turns out I ran into some malfunction bed files..