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A blast warning makes fur exit with status 1
Hello Bernhard,
When I run fur
on my laptop under WSL, I get this message:
fur - Failed Blast: Warning: [blastn] Number of threads was reduced to 4 to match the number of available CPUs
The program stops and returns no output at this point.
This happens unless I override the default -t 8
threads option of fur
with -t 4
. Indeed, my laptop has 4 threads, so the warning makes sense:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Address sizes: 46 bits physical, 48 bits virtual
Byte Order: Little Endian
CPU(s): 4
On-line CPU(s) list: 0-3
Vendor ID: GenuineIntel
Model name: 12th Gen Intel(R) Core(TM) i7-1270P
CPU family: 6
Model: 154
Thread(s) per core: 1
Core(s) per socket: 4
Socket(s): 1
If I run blastn
on 8 threads, it gives the same warning, changes the number of threads to 4 and continue running.
Well, this is fair enough, but I think the problem is a bit deeper than the default number of threads. I assume that log.Fatal()
apparently interprets any warnings from a run of blast
as fatal errors and forces an os.Exit(1)
. I think this issue is akin to the one Beatriz had last month, when there was a warning from blast
complaining about masking.
Cheers, ivan