Freebayes running for multiple days

Im trying to use the freebayes function on a 4.6gb Bam file. And so far its taken about 30 hours and its still processing. This is the biggest bam file I’ve done so far the others have been around 2gb, which usually have complete overnight. Is there something wrong?


Hi Patrick,
Is it done running ? Sometimes when jobs seem to take longer than expected, you can re-run it. The second run shouldn’t get stuck like the first.

Ill try an re run it now. The first run is still going. Its now been over 3 days so im assuming somethings wrong. Thanks


What is the organism you are calling variants on? If you have very high coverage at some regions (this can happen for variety of reasons including not deduplicating) Freebayes may get stuck.

Its a human. I dont think I have particularly high coverage, i have about 600k reads total with a mean coverage of about 1.2.