getting error - AssertionError ALL.reformatGeneFamilies.py

asgiraldoc commented 2 years ago

Dear all,

I'm trying to run your algorithm using my own data but I got this error:

agora-basic.py ../synteny/syntree.nwk ../synteny/orthologyGroups/orthologyGroups.%s.list ../synteny/genes/genes.%s.list

Inspect ancGenes/ancGenes.log for more information Status: 4 to do, 0 running, 0 done, 1 failed -- 5 total

Then, when I open that file for more information, this is the message:


------------------------------------------------------------------------
| Key               | Values                                           |
------------------------------------------------------------------------
| speciesTree       | ../synteny/syntree.nwk                           |
| orthologyGroups   | ../synteny/orthologyGroups/orthologyGroups.%s.list |
| IN.genesFiles     | ../synteny/genes/genes.%s.list                   |
| OUT.ancGenesFiles | ancGenes/all/ancGenes.%s.list.bz2                |
| OUT.genesFiles    | genes/genes.%s.list.bz2                          |
------------------------------------------------------------------------
Renaming the genes of M1 ... 4981 OK
Renaming the genes of M10 ... 5539 OK
Renaming the genes of M11 ... 5233 OK
Renaming the genes of M12 ... 5425 OK
Renaming the genes of M13 ... 4778 OK
Renaming the genes of M14 ... 5384 OK
Renaming the genes of M15 ... 5057 OK
Renaming the genes of M16 ... 4767 OK
Renaming the genes of M17 ... 5460 OK
Renaming the genes of M18 ... 6007 OK
Renaming the genes of M2 ... 4891 OK
Renaming the genes of M3 ... 4975 OK
Renaming the genes of M4 ... 4793 OK
Renaming the genes of M5 ... 5166 OK
Renaming the genes of M6 ... 5516 OK
Renaming the genes of M7 ... 5411 OK
Renaming the genes of M8 ... 5285 OK
Renaming the genes of M9 ... 4716 OK
Renaming the genes of A1 ... SKIPPING
Renaming the genes of A11 ... SKIPPING
Renaming the genes of A13 ... SKIPPING
Renaming the genes of A15 ... SKIPPING
Renaming the genes of A17 ... SKIPPING
Renaming the genes of A19 ... SKIPPING
Renaming the genes of A21 ... SKIPPING
Renaming the genes of A23 ... SKIPPING
Renaming the genes of A25 ... SKIPPING
Renaming the genes of A27 ... SKIPPING
Renaming the genes of A29 ... SKIPPING
Renaming the genes of A3 ... SKIPPING
Renaming the genes of A31 ... SKIPPING
Renaming the genes of A33 ... SKIPPING
Renaming the genes of A5 ... SKIPPING
Renaming the genes of A7 ... SKIPPING
Renaming the genes of A9 ... SKIPPING
Updating the ancestral families of A1 ... adding names ... 5969 OK
Updating the ancestral families of A11 ... adding names ... 5260 OK
Updating the ancestral families of A13 ... adding names ... Traceback (most recent call last):
  File "/home/asgiraldoc/Agora/src/ALL.reformatGeneFamilies.py", line 91, in <module>
    assert len(og) == len(set(og))
AssertionError

I'm not sure what's happening here... Can you help me? This is my data https://drive.google.com/drive/folders/1S6Ii0p2-nyc4EFWsc-3CjJZ_TohX3wek?usp=sharing

PD= when I ran the algorithm with your example data, everything was good.

Thank you,

alouis72 commented 2 years ago

Hi, it seems that you have genes that occurs twice in some orthogroups... As examples: M200000111300 occurs 2 times in orthologyGroups.A13.list line 305. M200001414100 in line 3976 extant genes should occurs only one time in orthogroups.

I hope that helps, best regards, Alexandra

asgiraldoc commented 2 years ago

Hi, yes, it worked. Thank you so MUCH.

DyogenIBENS / Agora

getting error - AssertionError ALL.reformatGeneFamilies.py #10