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jodyphelan / TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
GNU General Public License v3.0
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update_tbdb-Unable to update the database #376

Closed BhawnaY16 closed 5 months ago

BhawnaY16 commented 5 months ago

Hey, I have installed tbprofiler using bioconda and I was trying to update the database. I ma getting this error - TBProfiler version 4.3.0 (mytools) user@user-PowerEdge-R820:/media/user/36d81ee3-f383-4bc4-b619-20abd785be33$ tb-profiler update_tbdb

Running command: set -u pipefail; git checkout master

Running command: set -u pipefail; git pull

Running command: set -u pipefail; tb-profiler create_db --load Traceback (most recent call last): File "/home/user/miniconda3/envs/mytools/bin/tb-profiler", line 619, in args.func(args) File "/home/user/miniconda3/envs/mytools/bin/tb-profiler", line 200, in main_update_tbdb pp.run_cmd("tb-profiler create_db %s --load" % tmp) File "/home/user/miniconda3/envs/mytools/lib/python3.7/site-packages/pathogenprofiler/utils.py", line 397, in run_cmd raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,stderr.decode())) ValueError: Command Failed: set -u pipefail; tb-profiler create_db --load stderr: Traceback (most recent call last): File "/home/user/miniconda3/envs/mytools/bin/tb-profiler", line 619, in args.func(args) File "/home/user/miniconda3/envs/mytools/bin/tb-profiler", line 219, in main_create_db pp.create_db(args,extra_files=extra_files) File "/home/user/miniconda3/envs/mytools/lib/python3.7/site-packages/pathogenprofiler/db.py", line 556, in create_db mutation_lookup = get_snpeff_formated_mutation_list(args.csv,"genome.fasta","genome.gff",json.load(open("variables.json"))["snpEff_db"]) File "/home/user/miniconda3/envs/mytools/lib/python3.7/site-packages/pathogenprofiler/db.py", line 193, in get_snpeff_formated_mutation_list for row in csv.DictReader(open(csv_file)): FileNotFoundError: [Errno 2] No such file or directory: 'tbdb.csv' Cleaning up after failed run Do I need to manually create_db then update?How to resolve this error if you can please help

BhawnaY16 commented 5 months ago

Hey, I resolved it by making new conda env and downloading new tb-profiler version. Then I updated the database. I faced delly issue while processing my data, which I resolved by downloading delly and other few libraries.It worked!

Thanks

jodyphelan commented 5 months ago

Great to hear you have fixed this issue!