#3 TGICL - CAP3 unable to assemble due to seg fault

[ken]

Hi,
I'm really stuck in just one assembly which is holding up my whole project, and I'm hoping someone can provide a solution.

I have no problem with the clustering phase, but I'm running into a segmentation fault for one of my asm directories during assembly.

I've installed the 64-bit, Intel version of CAP3 as part of the TGICL pipeline. My server is running on Intel Xeon processors, and I can allocate up to 256 Gb of memory per node, but I don't think memory limitation is the problem.

Using 16 CPUS, all but one directory have assembled ok. In the asm_1 directory that runs into the error, this is what I get:

sh: line 1: 63326 Segmentation fault cap3 CL1 -p 93 > CL1.align
Error! cap3 failure detected (code=35584) on: CL1

It seg faults almost immediately when cap3 tries to assemble this cluster (other asm dirs are ok).
I have tried it independently (cap3 standalone) on just this directory as well, with the same error.

In contrast, I have another assembly which runs to completion just fine. The only difference is the size of the cluster.

Failed cluster:
1,359,975,661 bytes (1.35Gb)
962,144 sequences

Successful cluster:
1,135,345,720 bytes (1.1Gb)
731,031 sequences

The successful cluster ran on a 64Gb node, but the failed cluster gave seg fault even on 256Gb node.

So I think it's something in the cap3 (intel, 64bit) code, that is not allocating memory correctly when input is above certain size.

I might have to contact cap3 author to address this problem, but is there a way I can run the TGICL pipeline to make the cluster in the asm_1 directory smaller?

I am doing a comparison of assemblies, and all my other assemblies (over 20) have finished, and it is just this one that has stalled.

Please any help or advice would be greatly appreciated!
Please let me know if you require more info.

Best regards,
Ken

[ken]

I may have found a solution (described in the README), by doing containment clustering/assembly (sub clustering) of this largest cluster, running cap3 on it, and then combining with the initial cluster assemblies. It is not ideal as this would be the only assembly in my project with this extra level of processing, but I guess this is the only way?

Is there a tool or option in TGICL to generate the .singletons file containing the final list of all singletons?