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BenoitMorel / Asteroid

GNU Affero General Public License v3.0
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Bootstrapping error #11

Open barrettlab opened 6 months ago

barrettlab commented 6 months ago

Dear @BenoitMorel ,

Thanks for creating such a great program. I'm really interested to see how it performs on our data relative to other software (e.g. astral, astrid). Asteroid seems to have no issue building the best tree, but then aborts at the start of bootstrapping.

Input trees

bestparalog_treeshrink_output.txt

Output - best tree

asteroid_test_bestparalog.txt

I think this may be some issue on my end but can't figure out what it is.

Many thanks, Craig

(base) cbarrett@myco:/data/cbarrett/2024_Calypsoinae/hybpiper_2024_01_08/best_paralog/trimal/iqtree_bestparalog_treeshrink$ /usr/local/src/Asteroid/build/bin/asteroid -i bestparalog_treeshrink_output.treefile -p asteroidZZZZ.tre -r 10 -b 100 --use-gene-bl
--------------------------------------------------------------------------
[[13933,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: myco

Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
[00:00:00] Asteroid v1.0
Asteroid was called as follow:
/usr/local/src/Asteroid/build/bin/asteroid -i bestparalog_treeshrink_output.treefile -p asteroidZZZZ.tre -r 10 -b 100 --use-gene-bl

[00:00:00] Parsing gene trees...
[00:00:00] End of parsing gene trees
[00:00:00] Mapping gene to species...
[00:00:00] Extracting mappings from the gene trees...
[00:00:00] Computing coverage...
        Number of species: 44
        Total number of gene trees: 232
        Number of distinct coverage patterns:202
        Total number of gene leaves: 7418
        Sampling proportion: 0.726685
[00:00:00] Computing internode distances from the gene trees...

[00:00:00] Asteroid will now search for the best scoring tree from 10 starting trees
[00:00:00] Starting tree search 0
  score: -82.5065
[00:00:01] Starting tree search 1
  score: -82.5065
[00:00:04] Starting tree search 2
  score: -82.5065
[00:00:06] Starting tree search 3
  score: -82.5065
[00:00:08] Starting tree search 4
  score: -82.5065
[00:00:09] Starting tree search 5
  score: -82.5065
[00:00:12] Starting tree search 6
  score: -82.5065
[00:00:14] Starting tree search 7
  score: -82.5065
[00:00:15] Starting tree search 8
  score: -82.5065
[00:00:17] Starting tree search 9
  score: -82.5065
[00:00:19] Printing the best tree into asteroidZZZZ.tre.bestTree.newick

[00:00:19] Asteroid will now compute 100 bootstrap trees
asteroid: /usr/local/src/Asteroid/src/asteroid/asteroid.cpp:630: int main(int, char**): Assertion `arg.inputBSGeneTreeFile.size()' failed.
[myco:15721] *** Process received signal ***
[myco:15721] Signal: Aborted (6)
[myco:15721] Signal code:  (-6)
[myco:15721] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7fd599d8d390]
[myco:15721] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x38)[0x7fd5999e7438]
[myco:15721] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7fd5999e903a]
[myco:15721] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2dbe7)[0x7fd5999dfbe7]
[myco:15721] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x2dc92)[0x7fd5999dfc92]
[myco:15721] [ 5] /usr/local/src/Asteroid/build/bin/asteroid(main+0x1e69)[0x41b679]
[myco:15721] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fd5999d2840]
[myco:15721] [ 7] /usr/local/src/Asteroid/build/bin/asteroid(_start+0x29)[0x41c119]
[myco:15721] *** End of error message ***
Aborted (core dumped)
BenoitMorel commented 6 months ago

Hi Craig, Thanks a lot for your nice feedback. And thanks for the report, that was a really stupid mistake that I've made in my last commit... It's fixed now, you can git pull and recompile. Let me know if that works! Best, Benoit

Le mar. 20 févr. 2024 à 21:34, barrettlab @.***> a écrit :

Dear @BenoitMorel https://github.com/BenoitMorel ,

Thanks for creating such a great program. I'm really interested to see how it performs on our data relative to other software (e.g. astral, astrid). Asteroid seems to have no issue building the best tree, but then aborts at the start of bootstrapping.

Input trees

bestparalog_treeshrink_output.txt https://github.com/BenoitMorel/Asteroid/files/14350831/bestparalog_treeshrink_output.txt

Output - best tree

asteroid_test_bestparalog.txt https://github.com/BenoitMorel/Asteroid/files/14350853/asteroid_test_bestparalog.txt

I think this may be some issue on my end but can't figure out what it is.

Many thanks, Craig

(base) @.***:/data/cbarrett/2024_Calypsoinae/hybpiper_2024_01_08/best_paralog/trimal/iqtree_bestparalog_treeshrink$ /usr/local/src/Asteroid/build/bin/asteroid -i bestparalog_treeshrink_output.treefile -p asteroidZZZZ.tre -r 10 -b 100 --use-gene-bl

[[13933,1],0]: A high-performance Open MPI point-to-point messaging module was unable to find any relevant network interfaces:

Module: OpenFabrics (openib) Host: myco

Another transport will be used instead, although this may result in lower performance.

[00:00:00] Asteroid v1.0 Asteroid was called as follow: /usr/local/src/Asteroid/build/bin/asteroid -i bestparalog_treeshrink_output.treefile -p asteroidZZZZ.tre -r 10 -b 100 --use-gene-bl

[00:00:00] Parsing gene trees... [00:00:00] End of parsing gene trees [00:00:00] Mapping gene to species... [00:00:00] Extracting mappings from the gene trees... [00:00:00] Computing coverage... Number of species: 44 Total number of gene trees: 232 Number of distinct coverage patterns:202 Total number of gene leaves: 7418 Sampling proportion: 0.726685 [00:00:00] Computing internode distances from the gene trees...

[00:00:00] Asteroid will now search for the best scoring tree from 10 starting trees [00:00:00] Starting tree search 0 score: -82.5065 [00:00:01] Starting tree search 1 score: -82.5065 [00:00:04] Starting tree search 2 score: -82.5065 [00:00:06] Starting tree search 3 score: -82.5065 [00:00:08] Starting tree search 4 score: -82.5065 [00:00:09] Starting tree search 5 score: -82.5065 [00:00:12] Starting tree search 6 score: -82.5065 [00:00:14] Starting tree search 7 score: -82.5065 [00:00:15] Starting tree search 8 score: -82.5065 [00:00:17] Starting tree search 9 score: -82.5065 [00:00:19] Printing the best tree into asteroidZZZZ.tre.bestTree.newick

[00:00:19] Asteroid will now compute 100 bootstrap trees asteroid: /usr/local/src/Asteroid/src/asteroid/asteroid.cpp:630: int main(int, char): Assertion `arg.inputBSGeneTreeFile.size()' failed.[myco:15721] ** Process received signal [myco:15721] Signal: Aborted (6)[myco:15721] Signal code: (-6)[myco:15721] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7fd599d8d390][myco:15721] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x38)[0x7fd5999e7438][myco:15721] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7fd5999e903a][myco:15721] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2dbe7)[0x7fd5999dfbe7][myco:15721] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x2dc92)[0x7fd5999dfc92][myco:15721] [ 5] /usr/local/src/Asteroid/build/bin/asteroid(main+0x1e69)[0x41b679][myco:15721] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fd5999d2840][myco:15721] [ 7] /usr/local/src/Asteroid/build/bin/asteroid(_start+0x29)[0x41c119][myco:15721] End of error message Aborted (core dumped)

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barrettlab commented 6 months ago

Dear @BenoitMorel, the updated version worked beautifully. Many thanks! We study leafless heterotrophic plants, which are characterized by a lot of gene losses (i.e. missing data), so I think this approach will be particularly useful. Cheers, Craig