Maq takes forever to run

[RockChalkJayhawk]

Hey all. I've been trying to run maq map, but it seems like something isn't running right. It's been running for two days straight to align only one lane. I'm running a dual core AMDx64 with 4Gb RAM on 64-bit Ubuntu. It's only using 20-70% of my processor but constantly holding 3.5 Gb memory.

Any ideas? Is this normal? I thought it should only take ~17 hr.

[nilshomer]

Hey all. I've been trying to run maq map, but it seems like something isn't running right. It's been running for two days straight to align only one lane. I'm running a dual core AMDx64 with 4Gb RAM on 64-bit Ubuntu. It's only using 20-70% of my processor but constantly holding 3.5 Gb memory.

Any ideas? Is this normal? I thought it should only take ~17 hr.

How many reads? I would advise splitting it into 1-3 milllion read chunks since MAQ indexes the reads, thus is highly dependent on the # of input reads when it comes to memory etc.

[RockChalkJayhawk]

Slow Maq

How many reads? I would advise splitting it into 1-3 milllion read chunks since MAQ indexes the reads, thus is highly dependent on the # of input reads when it comes to memory etc.

It says that 8422536*2 reads were loaded, but this isn't PE data so does that mean I have 16M reads?

[nilshomer]

It says that 8422536*2 reads were loaded, but this isn't PE data so does that mean I have 16M reads?

You are correct, you have 8M paired end reads, and 16M "ends". Try splitting the data into 1-3M chunks and let me know how that goes.