Error while running Bismark-Mapper

[tims68]

Dear madam/sir,

Currently, I am setting up all the pre-processing steps for analyzing my cell-free DNA sequencing data, expected to arrive any time soon. While exploring all the possibilities for processing these WGBS samples, I ran into your paper. As I am still an inexperienced user of Ubuntu, I was quite impressed by your user-friendly interface which is perfectly substantiated by the associated Github protocol.

So far I was able to perform trimmomatic and fastqc on some practicing data. However, I am getting an error at the Bismark Mapper step. It looks like the bismark_genome_preparation worked (which I did separately from your pipeline because of memory issues), but when the single-end alignment starts, it keeps given the same error, see attachment of the .log file:

SRR6294810.log

It think there should be a easy solution as it seems like the error occurs with a simple "gzip" tool.

I used the following configuration set-up:

Hoping to hear from you soon.

Kind regards,
Tim