Message seen when performing alignment

Question

[K]

It's my first time doing alignment and I keep getting this message, is this normal?

[Pierre Lindenbaum]

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Answer 1

[GenoMax]

Yes this is normal.

[ATpoint]

Yes, normal and actually something that in 99.99% of cases you don't need. If you inspect the bwa mem C source code you'll see that you also cannot turn this off because the relevant lines miss an argument to respect the verbosity setting of bwa mem (which you should actually be able to set to make the tool less talky), so easiest is to simply ignore it.

For example, here is one line that you could turn off to be printed to screen when verbosity is 3 or higher:

https://github.com/lh3/bwa/blob/master/bwamem_pair.c#L91

And here is the stuff you see on screen without any verbosity switch:

https://github.com/lh3/bwa/blob/master/bwamem_pair.c#L97

[K]

Okay thank you, i have another question if you don't mind. How long will it take if my sample size R1&R2 is 53 gb each

[GenoMax]

It will take several hours (4-5 h with 8-12 cores). The time would be dependent on kind of hardware you have access to and performance of the storage system.

[K]

Oh if that's the case then maybe i am doing something wrong. It's been more than 15 hours since i started the process and still no sign of completing.

[ATpoint]

It depends on your storage, the memory available, the CPU speed, number of cores and to some extend on the experiment. I tend to remember that a 30x WGS sample took 12h on our high-performance cluster with 16 cores using a decent node. If the job runs (check by top) it is fine, get coffee and wait.

[K]

My workstation processor is intel xeon with 128 gb ram and 10 TB storage, it's an old computer.

[GenoMax]

Long as you are using multiple cores (Xeon should have them) you are maximizing the resource use. If you have an older computer and spinning disks then things can take long(er).

Answer 2

[Pierre Lindenbaum]

it's just an info/log https://github.com/lh3/bwa/blob/139f68fc4c3747813783a488aef2adc86626b01b/bwamem_pair.c#L97