segmentation fault

[kdahrens]

Hello,
I seem to be having a similar issue with the merge step as the previous user and I'm hoping you can help.

I was also receiving a "segmentation fault" error messages with a previous, smaller dataset when using an input file from rainbow div at default parameters. When I switched to this div code: rainbow div -i rcluster -o rbdiv.out -K 10 -f 0.5
I was able to get merge to work - presumably because it produced a slightly smaller input file. The number of clusters going into the div function were 205,189

Now, I am trying to run merge with a larger dataset of ~320 individuals with 296,456 clusters. No matter how I change the filtering parameters for the div function, I cannot get the merge step to work and receive the same "segmentation fault." I've tried both of the following:
rainbow merge -o rbasm.out -a -i rbdiv.out -r 2
rainbow merge -o rbasm.out -a -i rbdiv.out

Ideally, I want my input file to be from: rainbow div -i rcluster -o rbdiv.out -K 10 -f 0.5

Interestingly, when I use the same input file for the merge function, it does create an output file, always of the same size, and in the correct format. This is the same thing I was experiencing with my first, smaller dataset that I was finally able to troubleshoot as described above. Thus, I don't believe there is an issue with the input rbdiv file.

I can provide the rbdiv file if that's helpful. I've tried this with varying memory allocations (up to 256G) and it always stops creating the out file at the same line no matter how much I increase memory.

I see the discussion about adapters here. My sequences have been trimmed and QC'ed to remove adapters before this step. I'm not sure how that relates to what Rainbow does, but am relaying that information as well.

One more piece of info that may be helpful - here's the seff output from my sbatch script:

State: FAILED (exit code 139)
Cores: 1
CPU Utilized: 00:00:01
CPU Efficiency: 14.29% of 00:00:07 core-walltime
Job Wall-clock time: 00:00:07
Memory Utilized: 112.00 KB
Memory Efficiency: 0.00% of 256.00 GB