Felix Krueger

It also fails with `2.6.0`: ```nextflow ln: GSM7506206.fastq.gz: File exists ln: GSM7506206.fastq.gz: File exists ln: GSM7506206.fastq.gz: File exists ln: GSM7506206.fastq.gz: File exists ln: GSM7506206.fastq.gz: File exists ``` and the process...

hmm, is it sill doing something? Can you run `top` to see? Has it progressed to the bedGraph conversion step yet, or is it stuck at the extraction stage? You...

If anything I would probably try to bring it down to point where you are happy that it is alll still working as expected... maybe `--parallel 8`?

I am soooo sorry, I seem to have missed this issue entirely. The error 141 seems to come up every so often, and seems to go away mostly when Bowtie2...

Hi Antonio, Welcome to the world of methylation alignments! As a first comment, Accel Swift typically requires some [specific trimming](https://felixkrueger.github.io/Bismark/bismark/library_types/), namely ``` --clip_R1 10 --clip_R2 15 --three_prime_clip_R1 10 --three_prime_clip_R2 10...

Hmm, a 1% mapping efficiency is very low indeed. This typically happens either when you have the wrong library type (can you attache the R1/R2 FastQC base composition plots?), or...

Thanks for all these plots (they are from the 5' clipped samples, correct?). Overall they all look fine, there are no signs of technical or unexpected issues in the reads...

Yes, these warnings show up more frequently if you have short chromosomes or scaffolds. Typically the number is negligibly small, in your case ~0.05%. Just ignore. To interact with reads...

Thanks for the sample files. The sample seems to have been processed using the [Accel Swift kit](https://felixkrueger.github.io/Bismark/bismark/library_types/#swift), which introduces some hefty biases, especially at the start of Read 2: As...

wow that sounds like a huge amount of RAM. I don't think I have every heard about such excessive amounts... In theory, coverage2cytosine should hold the genome in memory (typically...