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chrisquince / STRONG

Strain Resolution ON Graphs
MIT License
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Error on Test data set with refactoring2 #66

Open chrisquince opened 4 years ago

chrisquince commented 4 years ago

So rerunning on the Test data after the recent merge fails with error:

Error in rule simplify_subgraphs: jobid: 0 output: subgraphs/Bin_ini/Bin_14/simplif.done

RuleException: AssertionError in line 46 of /mnt/gpfs/Hackathon/Test/STRONG/COG_pipe/HeavyLifting.snake. File "/mnt/gpfs/Hackathon/Test/STRONG/COG_pipe/HeavyLifting.snake", line 57, in __rule_simplify_subgraphs File "/mnt/gpfs/Hackathon/Test/STRONG/COG_pipe/HeavyLifting.snake", line 46, in bin_avg_cov File "/usr/lib/python3.5/concurrent/futures/thread.py", line 55, in run Exiting because a job execution failed. Look above for error message

However the bin coverage file seems fine?

chrisquince commented 4 years ago

OK I have found the origin of this bug. Sergey used input[0] in the snake which seems to be unreliable instead we need to point to correct input variable by name. In good git practice I am going to create a bugfixing branch off of master?

snurk commented 4 years ago

Sorry for late reply. Unfortunately I'm not sure whether named variables work within snakemake Python rules (all examples I've seen on the internet so far used input[0]). It's great if they do. Also I'm not sure that we should create branches for small bugfixes :)