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bmvdgeijn / WASP

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
Apache License 2.0
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No module named 'util' #87

Open viraj-rapolu opened 5 years ago

viraj-rapolu commented 5 years ago

Hello, I am using the mappability filtering pipeline of WASP, but am running into issues in Step 3 of the pipeline.

This is the command I am using: python find_intersecting_snps.py --is_paired_end --is_sorted --output_dir out/ --snp_tab tab.h5 --snp_index index.h5 --haplotype hap.h5 --samples my_samples.txt 54chr1.bam

This is the error output: File "find_intersecting_snps.py", line 10, in <module> import util ModuleNotFoundError: No module named 'util'

The version of WASP I am using was installed in July 2018. This issue persists when I use python 2.7, 3.5.1, and 3.6.6.

gmcvicker commented 5 years ago

It sounds like python is not finding the util module, possibly because your PYTHONPATH environment variable needs to be set. Try setting it to use the current directory and/or the directory that you installed WASP in. For example to add the current directory to the path enter the bash command: export PYTHONPATH=.:$PYTHONPATH