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A blast warning makes fur exit with status 1

Open IvanTsers opened this issue 5 months ago • 1 comments

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

IvanTsers avatar Sep 04 '24 08:09 IvanTsers