Tophat 2.0.6, empty insertions and deletion bed files

[iris_aurelia]

I've been using Tophat version 2.0.6 for a while and it seemed to work fine. However, today I wanted to use the insertions.bed and deletions.bed files but these files seemed to be empty after Tophat has finished. In previous versions of Tophat it worked fine.

Does anyone experience the same problem or does anybody know how to fix this problem?

[AsoBioInfo]

I encountered the same thing in the new version. It was working fine in the previous version. Did you find a fix for that?

[iris_aurelia]

No I haven't found a fix for that yet. I'm going to run a sample with the option --keep-tmp. There should be some temporary files being created regarding the indels.
In tophat 2.0.3. it was working fine, but since then these files are empty. I've tried the newest version 2.0.7, but this version doesn't output the indel files either.

[AsoBioInfo]

Even though by keeping the option --keep-tmp, yet I am encountering the unavailability of bed files...

[iris_aurelia]

Yes, same here, haven't really looked into it anymore. It looks like the segment_juncs step does report empty files:

Reported 8021 total potential splices
Reporting 0 potential deletions...
Reporting 0 potential insertions...
Reporting potential fusions...