star alignment failure (WSL2)

[Juami95]

I get the following error when I try to run the multi-step workflow:

Mar 24 16:20:52 ..... started STAR run
Mar 24 16:20:52 ..... loading genome
Mar 24 16:20:56 ..... processing annotations GTF
Mar 24 16:20:59 ..... inserting junctions into the genome indices
Mar 24 16:21:15 ..... started mapping
INFO [job mapping_reads] Max memory used: 4382MiB
WARNING [job mapping_reads] exited with status: 139
WARNING [job mapping_reads] completed permanentFail
WARNING [step mapping_reads] completed permanentFail
INFO [workflow ] completed permanentFail
{
    "alignments": {
        "location": "file:///home/jhmvangils/novice-tutorial-exercises/Aligned.sortedByCoord.out.bam",
        "basename": "Aligned.sortedByCoord.out.bam",
        "class": "File",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "size": 0,
        "path": "/home/jhmvangils/novice-tutorial-exercises/Aligned.sortedByCoord.out.bam"
    }
}
WARNING Final process status is permanentFail

I am running Ubuntu (18.04 or 20.04) on Windows 10, and have plenty of RAM (only 5 out of 16GB) at any point during the workflow, so I am not entirely sure where the error is coming from.

[mr-c]

Thanks @Juami95 ; I think this would have worked if we had configured WSL2 to allocate more memory.

Can you try the following on your laptop to see if this fixes the issue for you?

Windows users can configure WSL 2 to allocate more memory by opening the PowerShell and entering the following:

# turn off all wsl instances such as docker-desktop
wsl --shutdown

notepad "$env:USERPROFILE/.wslconfig"

In .wslconfig add the following

[wsl2]
memory=9GB

Save the file and right-click the Docker icon in the notifications area (or System tray) and then click "Restart Docker…"