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LUMC / HAMLET

RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department
MIT License
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ERROR : 'samples' #11

Closed elinashe closed 3 years ago

elinashe commented 3 years ago

while I'm running HAMLET, I've got the error which seems it can't read the samples. I replaced all reference file directories in 'test-hamlet-frankenstein.config' into my local directories, and when I manually test with command by using snakemake -n --snakefile Snakefile --configfile test/data/config/test-hamlet-frankenstein.config, it successfully passed.

This is the error what I've got. KeyError in line 29 of /node01data/shared/git/HAMLET/includes/qc-seq/Snakefile: 'samples' File "/node01data/shared/git/HAMLET/Snakefile", line 7, in File "/node01data/shared/git/HAMLET/includes/qc-seq/Snakefile", line 60, in File "/node01data/shared/git/HAMLET/includes/qc-seq/Snakefile", line 61, in File "/node01data/shared/git/HAMLET/includes/qc-seq/Snakefile", line 29, in get_readgroup_per_sample

Redmar-van-den-Berg commented 3 years ago

Can you paste the exact command you run and the configuration file you used when you got that error? It sounds like HAMLET cannot recognize the read groups for your samples.