Sebastian Uhrig

I no longer work at the DKFZ. You can send the link to this address instead: sebastian [dot] uhrig [at] googlemail [dot] com.

@YinYangKarly I had a look at the BAM file. The problem is with STAR, not with Arriba. STAR fails to report a chimeric alignment for the supporting reads. It either...

It would be best to open another issue about this if you don't mind.

Thanks for taking the time to create a stack trace. That's very helpful. A few things about Arriba's output look odd: - The reference files have non-standard names (`GRCh37.fa`, `ensembl.gtf`)....

Hi Melanie, This completely slipped my attention, sorry. Are you still interested in getting to the bottom of this? Since you cannot share the data, I would need your cooperation,...

Thanks for your willingness to get to the bottom of this issue. The first step is to find out at which point in the code the tool crashes. You need...

There is a high chance that the error is caused by one particular read. The output of the stack trace should confirm this. I have attached a modified version of...

This the output I expected. It fails in the function `align`, which aligns a read to the reference genome. Can you run the modified `arriba` executable and extract the alignments...

Apologies. I didn't think of you potentially using docker. Here is an executable that is compatible with docker: [arriba_with_read_name_output.zip](https://github.com/user-attachments/files/19226949/arriba_with_read_name_output.zip)

I may have found a fix. Can you please give the attached arriba version a spin? It should still print the read names, but should no longer crash. [arriba_with_read_name_output_fix.zip](https://github.com/user-attachments/files/19254179/arriba_with_read_name_output_fix.zip)