Excesively long execution time

[elcortegano]

I'm having issues with a large genome (2.7 Gb) sample, and I think the script might actually be stuck. It's been running for about two weeks now, with no output returned after "My what a large genome you have, this may take some time". The latest files updated in the output folder are *.delta and *.delta_filter (this one with a size of 0). These two files haven't changed apparently since the day the script started running. What's the script doing? what would be the expected execution time for a genome this length? is the script stuck? if possible, how to solve this?

MUM&Co was run as follows:

bash mumandco_v3.8.sh -r reference.fa -q sample.fa -g 2720000000 -o prefix -t 32 -b

Thanks!

[qdu-beep]

I'm having issues with a large genome (2.7 Gb) sample, and I think the script might actually be stuck. It's been running for about two weeks now, with no output returned after "My what a large genome you have, this may take some time". The latest files updated in the output folder are *.delta and *.delta_filter (this one with a size of 0). These two files haven't changed apparently since the day the script started running. What's the script doing? what would be the expected execution time for a genome this length? is the script stuck? if possible, how to solve this?

MUM&Co was run as follows:

bash mumandco_v3.8.sh -r reference.fa -q sample.fa -g 2720000000 -o prefix -t 32 -b

Thanks!

Hello， I have a similar situation. I think the -b parameter will take more time. How long does it take for your program to finish running? Best regards, Qiao

[elcortegano]

You are right the -b parameter might have been part of the problem here.

As for the runtime, cannot say, after weeks running I desisted and used an alternative approach.

[qdu-beep]

你是对的，参数可能是这里问题的一部分。-b

至于运行时，不能说，在运行了数周后，我停止了并使用另一种方法。

Hello,

Many thanks for your reply! I have desisted my program.

Best regards, Qiao