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Re: [last-align] Analysis Takes forever and times out on i386

Hi Martin,

First off, thanks for all your work on last-align upstream! :-)
See below:

On Tue, 22 Dec 2020 at 13:46, Frith, Martin <mcfrith@edu.k.u-tokyo.ac.jp> wrote:
Many thanks for this detailed problem report.

I believe that's an unintended (and surprising) problem, it should still work. The trouble is, it works on all my computers (I don't have a 32-bit arch). So it's hard for me to figure out.

You can maybe create an i386 chroot in an amd64 system, and test stuff there - this is how I'm testing it as well.

If you replace your command with:
$lastal -vvv humdb fuguMito.fa
(verbose mode), what does it print before hanging?

$lastal -vvv humdb fuguMito.fa
/usr/lib/last-align/lastal-plain: batch size=8192
/usr/lib/last-align/lastal-plain: calculating matrix probabilities...
/usr/lib/last-align/lastal-plain: matrix lambda=1.09861
/usr/lib/last-align/lastal-plain: matrix letter frequencies (upper=reference, lower=query):
A   C   G   T  
25  25  25  25
25  25  25  25
/usr/lib/last-align/lastal-plain: getting E-value parameters...
1.0960171987681839, 0.33538787507026158,
2.0290734315292083, -0.46514786408422282,
2.0290734315292083, -0.46514786408422282,
5.0543294182155085, 15.130999712620039,
5.0543294182155085, 15.130999712620039,
5.0543962679167036, 15.129930117400917

Hangs after this bit.

It would be great if you could test versions between 1145 and 1167 (e.g. by "hg update -r1155"). Of course I can't expect you to go to that trouble.

 I tried it for version 1155, and it times out with the exact same log I pasted above for 1167. Which means something broke between 1145 -1155.
Admittedly, I did not inspect any further.

Please let me know if you'd need any more information.

Thanks and regards


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