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Clinical-Genomics / microSALT

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
GNU General Public License v3.0
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ERROR - Reference update function failed prematurely. Review immediately #106

Closed patrikgrenfeldt closed 4 years ago

patrikgrenfeldt commented 4 years ago

Describe the bug Cronic detected failure for the command: /home/proj/production/servers/resources/hasta.scilifelab.se/crontabs/microsalt-start.sh

ERROR - Reference update function failed prematurely. Review immediately Traceback (most recent call last): File "/home/proj/bin/conda/envs/P_microSALT/bin/microSALT", line 8, in sys.exit(root()) File "/home/proj/bin/conda/envs/P_microSALT/lib/python3.6/site-packages/click/core.py", line 764, in call return self.main(args, kwargs) File "/home/proj/bin/conda/envs/P_microSALT/lib/python3.6/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/home/proj/bin/conda/envs/P_microSALT/lib/python3.6/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/proj/bin/conda/envs/P_microSALT/lib/python3.6/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/proj/bin/conda/envs/P_microSALT/lib/python3.6/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/proj/bin/conda/envs/P_microSALT/lib/python3.6/site-packages/click/core.py", line 555, in invoke return callback(args, *kwargs) File "/home/proj/bin/conda/envs/P_microSALT/lib/python3.6/site-packages/click/decorators.py", line 17, in new_func return f(get_current_context(), args, **kwargs) File "/home/proj/bin/conda/envs/P_microSALT/lib/python3.6/site-packages/microSALT/cli.py", line 396, in autobatch ext_refs.update_refs() File "/home/proj/bin/conda/envs/P_microSALT/lib/python3.6/site-packages/microSALT/utils/referencer.py", line 83, in update_refs self.fetch_external(self.force) File "/home/proj/bin/conda/envs/P_microSALT/lib/python3.6/site-packages/microSALT/utils/referencer.py", line 160, in fetch_external profile_no = re.search(r"\d+", sample[2]).group(0) AttributeError: 'NoneType' object has no attribute 'group'

RESULT CODE: 1

To Reproduce My guess on Steps to reproduce the behavior:

  1. Become hiseq.clinical
  2. Bash /home/proj/production/servers/resources/hasta.scilifelab.se/crontabs/microsalt-start.sh

Expected behavior No errors, all waiting microbial projects should have been started

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sylvinite commented 4 years ago

Issue due to pubMLST changing the text on their website. Code revised and pushed to production.