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CFSAN-Biostatistics / snp-pipeline

SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
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snp_filter.py fail #6

Closed gotero closed 7 years ago

gotero commented 7 years ago

Hi- I can't seem to get snp_filter.py to work. This is the error I get: $ snp_filter.py -n var.flt.vcf sampleDirectories.txt reference.fa Traceback (most recent call last): File "/Users/gotero/local/snp-pipeline/scripts/snp_filter.py", line 48, in snppipeline.remove_bad_snp(args_dict) AttributeError: 'module' object has no attribute 'remove_bad_snp'

The rest of the pipeline works fine, although I've only been running step-by-step workflows, not the all-in-one workflows. Here's the error I get when running "$setup.py test":

====================================================================== FAIL: test_1_snp_filter (test.test_snppipeline.SnpPipelineLambdaVirusTest) Run snp_filter and verify var.flt_preserved.vcf and var.flt_removed.vcf contains expected contents for each sample.

Traceback (most recent call last): File "/Users/gotero/local/snp-pipeline/test/test_snppipeline.py", line 168, in test_1_snp_filter self.run_function_test(snppipeline.remove_bad_snp, args_dict, os.path.join(dir, 'var.flt_removed.vcf')) File "/Users/gotero/local/snp-pipeline/test/test_snppipeline.py", line 98, in run_function_test self.assertTrue(new_timestamp > old_timestamp, "Old file was not overwritten with newer timestamp: %s" % file_to_compare) AssertionError: Old file was not overwritten with newer timestamp: samples/sample1/var.flt_removed.vcf

Ran 12 tests in 25.649s

FAILED (failures=1)

My environment: OS X v10.11.6 Python version = 2.7.12 |Anaconda 2.4.1 biopython 1.65 psutil 5.0.1 setuptools 27.2.0 PyVCF 0.6.8 Bowtie2 v2.2.6 samtools 1.3.1 varscan 2.3.7

Suggestions?

Thanks for creating and sharing a fantastic variant calling framework!

Glen

stevendavis commented 7 years ago

This smells like an install problem. I think you may have an old version of the snppipeline module. I recommend either upgrading or re-installing.

Upgrade

pip install --user --upgrade snp-pipeline

Reinstall

pip uninstall snp-pipeline pip install --user snp-pipeline

gotero commented 7 years ago

Looks like it was an install problem. I ran:

pip install --user --upgrade snp-pipeline

and it upgraded Biopython and setuptools. Initially I ran "$python setup.py developer", thinking that would do a complete install as well. Clearly not.

Thanks for the quick reply!

Glen

stevendavis commented 7 years ago

Happy to help. By the way, be sure to notice the new files generated in version 0.7.0. Closing this issue.