lighter installed from homebrew fails to complete

[rec3141]

I installed lighter 1.1.1 on MacOS 10.12.4 via homebrew and it repeatedly stalled after the 'storing trusted kmers' until I killed it after 10 minutes of 0% CPU usage. It started to write the corrected R1 reads before it stalled. I reinstalled from the github repo and it works fine. I'm not sure what the difference is.

[2017-06-30 11:12:18] =============Start====================
[2017-06-30 11:12:18] Scanning the input files to infer alpha(sampling rate)
[2017-06-30 11:12:44] Average coverage is 199.402 and alpha is 0.035
[2017-06-30 11:12:45] Bad quality threshold is "@"
[2017-06-30 11:13:33] Finish sampling kmers
[2017-06-30 11:13:33] Bloom filter A's false positive rate: 0.001737
[2017-06-30 11:17:45] Finish storing trusted kmers

[tseemann]

I think this is a CLANG+OpenMP vs GCC issue.

[andersgs]

It only works on Mojave if I give it one thread. @tseemann is on to something!

[tseemann]

@rec3141 what does brew linkage lighter say?

Try also brew reinstall -s -v lighter to build from source on your local machine.