Issue with memory and the gcsa index in toil-vg

Question

[jcmouren]

Hello,

I’m trying to construct a graph with toil-vg but have issues with memory and the gcsa indexing.

I would like to know how the values are determined in the follow-up error : “Requesting more disk than either physically available, or enforced by --maxDisk. Requested: 139586437120, Available: 133757087744”.

Is it really simply just disk memory ? Because I know I have way more than what is requested, so if anyone could explain it to me please.

Here’s the configuration I use : gcsa-index-mem: '230G' gcsa-index-disk: '130G' gcsa-index-preemptable: False

[Nitin Narwade]

I never used this tool but looking at the error you can try and set --maxDisk less than the available memory.

[jcmouren]

Yes but I need this much memory, and I don't get why it is saying I don't have enough available because if it's really disk memory I have several terabytes available

[Jouni Sirén]

Are you sure you have enough disk space available in the right directory? I have never used toil myself, but I believe it will use the local temporary directory as the working directory if you don't specify anything else.

[jcmouren]

Unfortunately I did specify the right directory and checked the disk space available. If I find an explanation by digging into the code I will update this post.