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dms-vep / dms-vep-pipeline-3

Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
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snakemake issue with the latest environment update #100

Closed Bernadetadad closed 8 months ago

Bernadetadad commented 8 months ago

@jbloom I'm getting the following Snakemake error for the latest pipeline when I run snakemake -j 16 --rerun-incomplete --software-deployment-method conda -s dms-vep-pipeline-3/Snakefile. I tired doing this from dms-vep-pipeline-3environments both on BloomLab and my own conda and I get the same error. 

Traceback (most recent call last):
  File "/home/bdadonai/miniconda3/envs/dms-vep-pipeline-3/lib/python3.11/site-packages/snakemake/cli.py", line 1893, in args_to_api
    dag_api = workflow_api.dag(
              ^^^^^^^^^^^^^^^^^
  File "/home/bdadonai/miniconda3/envs/dms-vep-pipeline-3/lib/python3.11/site-packages/snakemake/api.py", line 326, in dag
    return DAGApi(
           ^^^^^^^
  File "<string>", line 6, in __init__
  File "/home/bdadonai/miniconda3/envs/dms-vep-pipeline-3/lib/python3.11/site-packages/snakemake/api.py", line 436, in __post_init__
    self.workflow_api._workflow.dag_settings = self.dag_settings
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bdadonai/miniconda3/envs/dms-vep-pipeline-3/lib/python3.11/site-packages/snakemake/api.py", line 383, in _workflow
    workflow.include(
  File "/home/bdadonai/miniconda3/envs/dms-vep-pipeline-3/lib/python3.11/site-packages/snakemake/workflow.py", line 1379, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/fh/fast/bloom_j/computational_notebooks/bdadonai/2024/SARS-CoV-2_Omicron_BA.2_spike_DMS_COV3560/dms-vep-pipeline-3/Snakefile", line 32, in <module>
AssertionError
jbloom commented 8 months ago

It's actually due to an error in your barcode_runs CSV file, but the error message is not very helpful!

I am making a pull request right now in #101 to provide a better error message; when that is merged it should make it obvious how to fix this when you see the error message from updated pipeline (if it doesn't, then let me know).

jbloom commented 8 months ago

Run with the latest version of dms-vep-pipeline-3 and hopefully you will get a diagnosable error.