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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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My version is 4.3 and when I execute tb-profiler update_tbdb, the following message appears #287

Open jzhone opened 1 year ago

jzhone commented 1 year ago

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/seq/anaconda3/envs/tb4_3_copy/bin/tb-profiler", line 619, in args.func(args) File "/home/seq/anaconda3/envs/tb4_3_copy/bin/tb-profiler", line 200, in main_update_tbdb pp.run_cmd("tb-profiler create_db %s --load" % tmp) File "/home/seq/anaconda3/envs/tb4_3_copy/lib/python3.9/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: Don't know how to handle this mutation: tlyA frameshift_variant

Cleaning up after failed run

jodyphelan commented 1 year ago

Hi @jzhone

Between v4.3 and v4.4 there were a few changes which make the DB from github incompatible with older versions. I would try upgrade to v4.4.2 and check if that works for you.

jzhone commented 1 year ago

Thanks for reply. Can I update the version via conda update? Or do I need to rebuild the new environment to install it with conda.

jodyphelan commented 1 year ago

I would recommend to build a new environment with conda