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dieterich-lab / rp-bp

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.
MIT License
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'str' object has no 'keys' attribute #94

Closed m-swirski closed 6 years ago

m-swirski commented 6 years ago

I have encountered following error at the merging replicates step. Could anything be done about this? rp-bp_error2

eboileau commented 6 years ago

Dear @Miswi, this is most likely because your configuration yaml file is mis-formatted. In particular, take a look at the key riboseq_biological_replicates: in the example configuration file.

m-swirski commented 6 years ago

The only difference I could spot is lack of ':' after biological replicates names. (in 'c-elegans-test:'). I have, however, successfully ran the pipeline with --run-replicates flag for 22 fastq files, so repeating whole process would be waste of time. run-all-rpbp-instances with corrected .yaml file will do the job?

eboileau commented 6 years ago

If you do NOT use the overwrite flag, then the program will not recreate existing files, so it is good to ensure that these are indeed correct. The resulting warnings are then only informative. Yes, you can use run_all_rpbp_instances without the --run-replicates, and only using --merge-replicates, with the correctly formatted configuration file.

m-swirski commented 6 years ago

Great, it seems to be working, thanks for support