ERROR: wrote file wastral_top37geneTrees_ed.sptree ..

[4br4ha4mRR]

Dear get_phylomarkers team

Recently, I conducted an analysis using get_phylomarkers based on the core genome calculated through get_homologues, and in the final part of the analysis, it abruptly terminates specifically here:

wrote file wastral_top37geneTrees_ed.sptree ...
826 check_output /home/rot3cksxot3/get_phylomarkers/lib/get_phylomarkers_fun_lib
<= exiting check_output ...
10:49:12 523 run_ASTRAL /home/rot3cksxot3/get_phylomarkers/lib/get_phylomarkers_fun_lib

I ran the analysis with the -D 2 option and am attaching the log file.
get_phylomarkers_run_AIR1tDNA_k1.0_m0.7_Thigh_11Sep24.log

I wonder if you could help me with this issue.

I look forward to hearing from you.

Sincerely,

[eead-csic-compbio]

Hi @4br4ha4mRR , sorry for the delay. If you still have them, it might help checking the files astral4.log and wastral.log

[4br4ha4mRR]

Hello, don’t worry, I’m attaching the log files.
wastral.log
astral4.log

[4br4ha4mRR]

wastral_usertree_concat_model_selection.log

[eead-csic-compbio]

wastral_usertree_concat_model_selection.log

Thanks, while checking this log file I found the following IQTREE errors:

ERROR: For your convenience alignment with variable sites printed to wastral_usertree_concat_model_selection.varsites.phy
ERROR: Invalid use of +ASC because of 5 invariant sites in the alignment

These have been the subject of threads such as iqtree/iqtree2#74 , so we need to further debug to rule out any errors before IQTREE and then see if other versions are not affected, what do think @vinuesa ?