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chrisquince / STRONG

Strain Resolution ON Graphs
MIT License
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Assertion error is ugly way to end dryrun #67

Closed chrisquince closed 4 years ago

chrisquince commented 4 years ago

OK so currently in a clean dryrun the snake will run up to the assertion error below. That is because that file is empty. Maybe we replace the assertion with warning of empty file so that the dryrun continues?

Full Traceback (most recent call last): File "/usr/local/lib/python3.5/dist-packages/snakemake/init.py", line 401, in snakemake print_compilation=print_compilation) File "/usr/local/lib/python3.5/dist-packages/snakemake/workflow.py", line 743, in include exec(compile(code, snakefile, "exec"), self.globals) File "/mnt/gpfs/Hackathon/Test/STRONG/COG_pipe/BayesAGraph.snake", line 11, in else read_selected_bins("subgraphs/Merged_Bin/selected_bins.txt") File "/mnt/gpfs/Hackathon/Test/STRONG/COG_pipe/BayesAGraph.snake", line 7, in read_selected_bins print("Reading selected bins from %s" % fn) AssertionError

AssertionError in line 6 of /mnt/gpfs/Hackathon/Test/STRONG/COG_pipe/BayesAGraph.snake. File "/mnt/gpfs/Hackathon/Test/STRONG/COG_pipe/BayesAGraph.snake", line 11, in File "/mnt/gpfs/Hackathon/Test/STRONG/COG_pipe/BayesAGraph.snake", line 6, in read_selected_bins

snurk commented 4 years ago

Not sure about this particular problem, but I'm not sure that we can have a reasonable dryrun behavior, since we have a lot of places where we re-evaluate the targets based on the output we get.

chrisquince commented 4 years ago

OK maybe this is not such an issue.