Mhap overlap jobs fail

[JWrighty97]

Good evening,

I am running Canu on a remote desktop running a WSL.

The code I inputted to run the command was: canu -p canu_assem -d canu2 genomeSize=1.6g useGrid=false -nanopore nano_cat_filt.fastq.gz maxMemory=188 maxThreads=32 corMemory=16 cnsMemory=16 as when I tried initially running it cor and cns were not being allocated memory and now I am hitting this error

-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Tue Nov 26 20:02:58 2024 with 1002.719 GB free disk space (297 processes; 2 concurrently)

    cd correction/1-overlapper
    ./mhap.sh 1 > ./mhap.000001.out 2>&1
    ./mhap.sh 2 > ./mhap.000002.out 2>&1

-- Finished on Sun Nov 24 05:37:06 2024 (60155 seconds) with 998.261 GB free disk space
----------------------------------------
--
-- Mhap overlap jobs failed, retry.
--   job correction/1-overlapper/results/000004.ovb FAILED.
--   job correction/1-overlapper/results/000005.ovb FAILED.

And then it runs a second time but then give us. Any help would be much appreciated

[skoren]

I suspect this is an issue with the WSL not supporting all linux functionality, most likely named pipes (see #2167 and #2306). What's in the failed job logs (mhap.*.out)? If it is the pipe naming, you can add mhapPipe=False to work around the WSL limitation.