bodhi84

I too have the same error. The junction files contained strand information, but it is still showing the error. GL000225.1:+..chr11:-..KI270317.1:+..KI270519.1:-..GL000205.2:-..KI270711.1:-..KI270303.1:+..chr22:-..chr10:-..KI270755.1:+..KI270315.1:-..KI270316.1:+..KI270364.1:+..GL000221.1:+..KI270522.1:+..KI270336.1:-..KI270714.1:+..chr21:+..KI270589.1:-..chr12:+..chr4:+..chr1:+..KI270727.1:-..KI270590.1:+..KI270448.1:+..KI270311.1:-..GL000220.1:-..KI270333.1:+..KI270522.1:-..KI270752.1:+..KI270717.1:-..Traceback (most recent call last): File "leafcutter/clustering/leafcutter_cluster_regtools.py", line 534, in main(options,...

Hi Jack, It worked fine after I used the --checkchrom flag. Bodhi