Difficulty in using OrthoFinder

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21

I think what is going on is that only the first part of the updated tool was wrapped in Galaxy. The parts up until the “grouping” step.

Now, I don’t know why this didn’t go further. It looks like a researcher from the AU BioCommons group was working on it in collaboration with the EU team. Maybe that was all that they needed or had time for back then.

Let’s ask one of the devs – @bernt-matthias do you know if there are plans for wrapping the remainder of this tool suite? Or suggestions for alternative tools? The goal is paralogs.

22

In order to make sense of the tool outputs it might make sense to check the sources.

The from_work_dir (resp directory`) attributes tell which files the tool uses for the output and the label attribute how Galaxy labels it.

I will check if there are other files that Galaxy ignores at the moment.

23

I checked our tool tests. In full mode there are a few files/folders that match “ortho*“:

results/Species_Tree/Orthogroups_for_concatenated_alignment.txt
results/Orthogroups
results/Orthogroups/Orthogroups.tsv
results/Orthogroups/Orthogroups.GeneCount.tsv
results/Orthogroups/Orthogroups_SingleCopyOrthologues.txt
results/Orthogroups/Orthogroups_UnassignedGenes.tsv
results/Orthogroups/Orthogroups.txt
results/Orthologues
results/Orthologues/Orthologues_Mycoplasma_gallisepticum.faa
results/Orthologues/Orthologues_Mycoplasma_genitalium.faa
results/Orthologues/Orthologues_Mycoplasma_agalactiae.faa
results/Orthologues/Orthologues_Mycoplasma_hyopneumoniae.faa
results/Orthogroup_Sequences
results/Comparative_Genomics_Statistics/OrthologuesStats_Totals.tsv
results/Comparative_Genomics_Statistics/OrthologuesStats_one-to-many.tsv
results/Comparative_Genomics_Statistics/OrthologuesStats_many-to-one.tsv
results/Comparative_Genomics_Statistics/OrthologuesStats_one-to-one.tsv
results/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv
results/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv
results/WorkingDirectory/OrthoFinder_graph.txt

The full output of the Orthologues directory is

results/Orthologues/
├── Mycoplasma_agalactiae.faa.tsv
├── Mycoplasma_gallisepticum.faa.tsv
├── Mycoplasma_genitalium.faa.tsv
├── Mycoplasma_hyopneumoniae.faa.tsv
├── Orthologues_Mycoplasma_agalactiae.faa
│   ├── Mycoplasma_agalactiae.faa__v__Mycoplasma_gallisepticum.faa.tsv
│   ├── Mycoplasma_agalactiae.faa__v__Mycoplasma_genitalium.faa.tsv
│   └── Mycoplasma_agalactiae.faa__v__Mycoplasma_hyopneumoniae.faa.tsv
├── Orthologues_Mycoplasma_gallisepticum.faa
│   ├── Mycoplasma_gallisepticum.faa__v__Mycoplasma_agalactiae.faa.tsv
│   ├── Mycoplasma_gallisepticum.faa__v__Mycoplasma_genitalium.faa.tsv
│   └── Mycoplasma_gallisepticum.faa__v__Mycoplasma_hyopneumoniae.faa.tsv
├── Orthologues_Mycoplasma_genitalium.faa
│   ├── Mycoplasma_genitalium.faa__v__Mycoplasma_agalactiae.faa.tsv
│   ├── Mycoplasma_genitalium.faa__v__Mycoplasma_gallisepticum.faa.tsv
│   └── Mycoplasma_genitalium.faa__v__Mycoplasma_hyopneumoniae.faa.tsv
└── Orthologues_Mycoplasma_hyopneumoniae.faa
    ├── Mycoplasma_hyopneumoniae.faa__v__Mycoplasma_agalactiae.faa.tsv
    ├── Mycoplasma_hyopneumoniae.faa__v__Mycoplasma_gallisepticum.faa.tsv
    └── Mycoplasma_hyopneumoniae.faa__v__Mycoplasma_genitalium.faa.tsv

The first lines of eg `Mycoplasma_agalactiae.faa.tsv` are

Orthogroup      Species Mycoplasma_gallisepticum.faa    OrthologsOG0000002       Mycoplasma_agalactiae.faa       gi|31541629|gb|AAP56929.1|      gi|290752802|emb|CBH40777.1|OG0000002       Mycoplasma_hyopneumoniae.faa    gi|31541629|gb|AAP56929.1|      gi|71851738|gb|AAZ44346.1|OG0000002       Mycoplasma_genitalium.faa       gi|31541629|gb|AAP56929.1|      gi|3844775|gb|AAC71398.1|OG0000002       Mycoplasma_genitalium.faa       gi|284811859|gb|AAP56391.2|     gi|3845003|gb|AAC71638.1|OG0000002       Mycoplasma_agalactiae.faa       gi|31541268|gb|AAP56569.1|      gi|290752526|emb|CBH40498.1|OG0000002       Mycoplasma_hyopneumoniae.faa    gi|31541268|gb|AAP56569.1|      gi|71851837|gb|AAZ44445.1|OG0000002       Mycoplasma_genitalium.faa       gi|31541268|gb|AAP56569.1|      gi|1045987|gb|AAC71511.1|OG0000002       Mycoplasma_hyopneumoniae.faa    gi|31541070|gb|AAP56372.1|      gi|144227640|gb|AAZ44535.2|OG0000002       Mycoplasma_agalactiae.faa       gi|31541070|gb|AAP56372.1|      gi|290753081|emb|CBH41057.1|OG0000002       Mycoplasma_genitalium.faa       gi|31541070|gb|AAP56372.1|      gi|3845064|gb|AAC72489.1|, gi|1045740|gb|AAC71283.1|OG0000002       Mycoplasma_agalactiae.faa       gi|284812058|gb|AAP56715.2|     gi|290752592|emb|CBH40564.1|, gi|290752894|emb|CBH40869.1|

And eg Mycoplasma_agalactiae.faa__v__Mycoplasma_gallisepticum.faa.tsv

Orthogroup      Mycoplasma_agalactiae.faa       Mycoplasma_gallisepticum.faa
OG0000002       gi|290752802|emb|CBH40777.1|    gi|31541629|gb|AAP56929.1|
OG0000002       gi|290752526|emb|CBH40498.1|    gi|31541268|gb|AAP56569.1|
OG0000002       gi|290753081|emb|CBH41057.1|    gi|31541070|gb|AAP56372.1|
OG0000002       gi|290752592|emb|CBH40564.1|, gi|290752894|emb|CBH40869.1|      gi|284812058|gb|AAP56715.2|

We could add any of these files to the outputs. Just let us know if any of these would be of help.

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24

Those files look like what I would be interested in if I was doing this! Both the single line summary and the parsed (even though either could create the other). Thanks @bernt-matthias

What do you think @jaredbernard and @Sutrisha_Kundu – I think this is what both of you were looking for. Any preferences or comments?

25

Thanks for looking into this @bernt-matthias and @jennaj! Yes, those are precisely the output files I was looking for.

26

Yes yes exactly this. Thank you for clarifying and finding it out. I was looking for exactly these all output files.

27

The missing outputs should become available in the next version of the orthofinder Galaxy tool (2.5.5+galaxy1): Orthofinder improvements by bernt-matthias · Pull Request #7213 · galaxyproject/tools-iuc · GitHub

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