Open MelanieBroutin opened 1 year ago
Thanks for taking the time to create a stack trace. That's very helpful.
A few things about Arriba's output look odd:
GRCh37.fa
, ensembl.gtf
). Also, Arriba complains about malformed blacklist entries. While it is possible to use your own reference files, it may be that you accidentally mixed up files or generated corrupted files. Perhaps the BAM file and reference files have incompatible coordinate systems (GRCh37 vs. GRCh37). Please double-check that your files are compatible or try the reference files created by the script download_referencrs.sh
.Thanks for this quick reply. I am used to use arriba in routine. So I processed a lot of samples already with this version of arriba and without any issue. I used the same reference files as always. I use the arriba provided in arriba.tar.gz in https://github.com/suhrig/arriba/releases/tag/v2.4.0. I have compiled arriba by myself only for debugging it with gdb. The sample is an Illumina RNAseq with UMI. I could not share the sample with you as it is patient data.
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, meaning possibly a few rounds of running a modified Arriba with debug logging where each iteration gets us closer to the root cause. Alternatively, if you can reproduce the error on a minimal dataset, for example on just the reads around the breakpoint which triggers the error, this should be harmless to share since there is only little likelihood that identifiable information would be shared. I could send you commands to extract the reads from around the fusion breakpoints if you like. Let me know which option you prefer.
Best regards, Sebastian
Hello,
I have an error
Segmentation fault
when I run arriba v2.4.0. I tried to debug with gdb.Below, you can find all the logs.
Do you know why I have this error ?
Thank you