Frequently asked questions

What you mean with baltica provides a interface between users and DJU methods:

There are many specificities to the DJU methods, and while running one method is not too complicated, figuring out how to run multiple methods is time-demanding. Baltica aims to facilitate this task so that methods results can be produced and compared.

Snakemake Error: Directory cannot be locked.:

This error happens when there is an error or failure during the workflow execution, and Snakemake's process does not have the opportunity to unlock the directory. Use baltica <workflow> <config> --unlock to resolve it. See more here

ERROR lines in majiq_gtf_to_gff:

Most of the errors in this rules are not fatal. See here for the diagnostics.

rmats empty or mostly empty outputs

This error can be either issue with: - The read length parameter. To resolve it, increase the read length parameter or use --variable-read-length in Baltica configuration. - Or an error with the stack size limit. To resolve it increase the stack size in bash with ulimit -c unlimited.

Junctionseq bpapply error:

This error occurs in the junctionseq_analysis rule, which uses multiple threads with BiocParallel. One can overcome this issue by setting threads to 1 on the said rule.

Junctionseq analysis thread error

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index xxx out of bounds for length xxx It is complaining the maximum read length is longer than the read length input. First, check the maximum read length in the quality control report and then increase the read_len parameter on Baltica config.

How does Baltica compute the score for each DJU method?

The different DJU methods are pretty different in many aspects, including how they compute the final test statistic, and we use the following rule to compute the score for the Baltica table (higher is better):
- majiq score = 1 - non-changing-threshold (probability of |ΔΨ| > 0.2, by default)
- leafcutter = 1 - p.adjust
- junctionseq = 1 - padjust
- rmats = 1 - FDR

I see a message: /bin/bash: /root/.bashrc: Permission denied. What is wrong?

This error message is benign and, in our experience, does not affect workflow execution.