jodyphelan
commented
1 year ago It looks like loading the database did not work. I think this may be a bug with the version. Could you try add --load to your create_db command? and then just using --db tbdb_1 in your profile command?
Alternatively you could try upgrade to the latest version (v4.4.0)
Describe the bug Am using TB-profiler 4.2.0 on a shared server to create a custom_db using this command "tb-profiler create_db -p tbdb_1 --custom --include_original_mutation" and it seem to have created all the necessary files (json,fasta etc). I moved all these new files to a new directory 'TEST'.
When i tried running ' tb-profiler profile --external_db TEST/tbdb_1 -1 R1.fastq.gz -2 R2.fastq.gz -p TE --txt', I get this error set -u pipefail; rm ./9c8988dc-ad47-4c6e-80e2-b525b470ceb4_1U ./9c8988dc-ad47-4c6e-80e2-b525b470ceb4_2U Traceback (most recent call last): File "/mnt/transient_data/conda/envs/tb-profiler/bin/tb-profiler", line 566, in
args.func(args)
File "/mnt/transient_data/conda/envs/tb-profiler/bin/tb-profiler", line 150, in main_profile
results.update(pp.run_profiler(args))
File "/mnt/transient_data/conda/envs/tb-profiler/lib/python3.9/site-packages/pathogenprofiler/cli.py", line 36, in run_profiler
args.bam_file = get_bam_file(args)
File "/mnt/transient_data/conda/envs/tb-profiler/lib/python3.9/site-packages/pathogenprofiler/cli.py", line 106, in get_bam_file
ref_file=args.conf["ref"], prefix=args.files_prefix,sample_name=args.prefix,
TypeError: 'NoneType' object is not subscriptable
Cleaning up after failed run
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
File "/mnt/transient_data/conda/envs/tb-profiler/bin/tb-profiler", line 36, in cleanup
O.write("* Database version: %s\n" % args.conf["version"]["commit"]) if "conf" in vars(args) else ""
TypeError: 'NoneType' object is not subscriptable
What might be the issue?? thanks