cufflinks without reference stopped at chrM

[arrchi]

My code is as simple as this:

cufflinks -o test accepted_hits.bam

The bam file was generated by tophat. Both tophat and Cufflink are the latest version (1.3 and 1.03).

Without a reference, cufflinks stop and here is the last output:

Processing Locus chr9:141152985-141153035 [***************** ]> Processing Locus chrM:0-16571 [************************ ] 97%

I tried cufflinks (v 1.0.2). I saw the same problem.

However, if I use cufflinks with a reference, the program runs smoothly without this problem.

Any suggestion?

Thanks in advance.

[arrchi]

I checked cufflinks output , there is no chrX, chrY and chrM in the three output files. But my input bam file does have these three chromosome info.

Any ideas? please!

[arrchi]

One of my several cufflinks programs does finished after stuck at chrM for about one day. So i guess it just needs a little bit more time and patience.

[steven]

OK, that's probably because chrM is often overloaded with reads

[baritone]

The problem is still there

And I'm posting this in the year of 2016

[GenoMax]

And I'm posting this in the year of 2016

Even with latest cufflinks version?