Consistent error: if (is.na(gsParam$synteny$hogs)) { : argument is of length zero

[Toffeeladd]

Hi, thanks for such a great program. I am getting the same issue as #75 and #165

I am having exactly the same issue when using orthofinder 2.5.5 with R 4.4.2 and GENESPACE 1.3.1 via WSL. I am running orthofinder outside of Genespace and then copying the results into the wd/. run_genespace() was working the first time when testing on 3 genomes and continues to work if I run with the original orthofinder output.

Now I am doing a much larger run with 43 genomes and a new orthofinder run (which completed successfully) I'm consistently getting if (is.na(gsParam$synteny$hogs)) { : argument is of length zero

This is the full error for context:

1. Running orthofinder (or parsing existing results) Checking for existing orthofinder results ... [1] FALSE ... found existing run, not re-running orthofinder Error in if (is.na(gsParam$synteny$hogs)) { : argument is of length zero

I have tried:

• Deleting all the previous runs (like others who have run into this error suggested)
• Reinstalling Genespace R package multiple times
• Copying N0.tsv directly to the wd/results
• Reinstalling R and rebuilding all packages

I understand running on 43 genomes is alot and I have not seen any other people using it for that many genomes. I am less interested in the plots and more in pan_genes outputs.

If you have any suggestions to how to work around this error I would really appreciate it.

[jtlovell]

hmm. before we try anything else, can you do this:

ofRes <- find_ofFiles("path/to/orthofinder/run")
print(ofRes$hogs)

[Toffeeladd]

Thanks for getting back so quickly.

This finds the N0.tsv file and puts it in wd/results but a subsequent run still does not work and returns the same error

ofRes <- find_ofFiles("/mnt/c/Users/username/Documents/PhD/GENESPACE/input_files/wd/orthofinder")
> print(ofRes$hogs)
[1] "/mnt/c/Users/username/Documents/PhD/GENESPACE/input_files/wd/orthofinder/Results_Nov12/Phylogenetic_Hierarchical_Orthogroups/N0.tsv"

[jtlovell]

Hmm ... so when you run init_genespace, you get no errors, then when you run run_genespace, it errors out with "Error in if (is.na(gsParam$synteny$hogs)) {...".

Can you run this:

test <- init_genespace(...) # add the parameters you used previously
synParam <- set_syntenyParams(test)
print(synParam$synteny$hogs)

[Toffeeladd]

Correct no errors with init_genespace and the error is only in run_genespace

I ran the above code:

test <- init_genespace(
+   wd = wd,
+   path2mcscanx = path2mcscanx)
Checking Working Directory ... PASS: `/mnt/c/Users/username/Documents/PhD/GENESPACE/input_files/wd`
Checking user-defined parameters ...
        Genome IDs & ploidy ...
                Brassica_oleracea_var_italica       : 1
                Brassica_oleracea                   : 1
                Brassica_rapaZ1                     : 1
                Brassica_tournefortii               : 1
                Citrullus_lanatus_subsp.cordophanus : 1
                Citrullus_lanatus_subsp.vulgaris    : 1
                Citrullus_mucosospermus             : 1
                Citrus_ichangensis                  : 1
                Citrus_linwuensis                   : 1
                Citrus_reticulata                   : 1
                Coix_aquatica                       : 1
                Fagopyrum_esculentum                : 1
                Fagopyrum_homotropicum              : 1
                Fallopia_multiflora                 : 1
                Hordeum_marinum                     : 1
                Hordeum_vulgare_cultivar            : 1
                Hordeum_vulgare_wild_type           : 1
                Juglans_californica                 : 1
                Juglans_cinerea                     : 1
                Juglans_nigra                       : 1
                Oryza_barthii                       : 1
                Oryza_rufipogon                     : 1
                Oryza_sativa                        : 1
                Panicum_hallii                      : 1
                Prunus_davidiana                    : 1
                Prunus_mira                         : 1
                Prunus_persica                      : 1
                Setaria_itallica                    : 1
                Setaria_viridis                     : 1
                Solanum_buesii                      : 1
                Solanum_candolleanum                : 1
                Solanum_galapagense                 : 1
                Solanum_lycopersicum                : 1
                Solanum_pimpinellifolium            : 1
                Solanum_tuberosum_PG6247            : 1
                Sorghum_bicolor_ssp.verticilliflorum: 1
                Sorghum_bicolor                     : 1
                Vitis_labrusca                      : 1
                Vitis_vinifera_cultivated           : 1
                Vitis_vinifera_ssp.sylvestris       : 1
                Zea_luxurians                       : 1
                Zea_mays_subsp.parviglumis          : 1
                Zea_MaysB73                         : 1
        Outgroup ... NONE
        n. parallel processes ... 6
        collinear block size ... 5
        collinear block search radius ... 25
        n gaps in collinear block ... 5
        synteny buffer size... 100
        only orthogroups hits as anchors ... TRUE
        n secondary hits ... 0
Checking annotation files (.bed and peptide .fa):
        Brassica_oleracea_var_italica       : 56434 / 56434 geneIDs exactly match (PASS)
        Brassica_oleracea                   : 57044 / 57044 geneIDs exactly match (PASS)
        Brassica_rapaZ1                     : 51013 / 51013 geneIDs exactly match (PASS)
        Brassica_tournefortii               : 41739 / 41739 geneIDs exactly match (PASS)
        Citrullus_lanatus_subsp.cordophanus : 20910 / 20910 geneIDs exactly match (PASS)
        Citrullus_lanatus_subsp.vulgaris    : 20540 / 20540 geneIDs exactly match (PASS)
        Citrullus_mucosospermus             : 20609 / 20609 geneIDs exactly match (PASS)
        Citrus_ichangensis                  : 30458 / 30458 geneIDs exactly match (PASS)
        Citrus_linwuensis                   : 30306 / 30306 geneIDs exactly match (PASS)
        Citrus_reticulata                   : 27312 / 27312 geneIDs exactly match (PASS)
        Coix_aquatica                       : 35123 / 35123 geneIDs exactly match (PASS)
        Fagopyrum_esculentum                : 36119 / 36119 geneIDs exactly match (PASS)
        Fagopyrum_homotropicum              : 38796 / 38796 geneIDs exactly match (PASS)
        Fallopia_multiflora                 : 41409 / 41409 geneIDs exactly match (PASS)
        Hordeum_marinum                     : 41011 / 41011 geneIDs exactly match (PASS)
        Hordeum_vulgare_cultivar            : 49046 / 49046 geneIDs exactly match (PASS)
        Hordeum_vulgare_wild_type           : 54365 / 54365 geneIDs exactly match (PASS)
        Juglans_californica                 : 31263 / 31263 geneIDs exactly match (PASS)
        Juglans_cinerea                     : 31432 / 31432 geneIDs exactly match (PASS)
        Juglans_nigra                       : 31500 / 31500 geneIDs exactly match (PASS)
        Oryza_barthii                       : 37113 / 37113 geneIDs exactly match (PASS)
        Oryza_rufipogon                     : 41967 / 41967 geneIDs exactly match (PASS)
        Oryza_sativa                        : 38055 / 38055 geneIDs exactly match (PASS)
        Panicum_hallii                      : 31994 / 31994 geneIDs exactly match (PASS)
        Prunus_davidiana                    : 29085 / 29085 geneIDs exactly match (PASS)
        Prunus_mira                         : 28070 / 28070 geneIDs exactly match (PASS)
        Prunus_persica                      : 27894 / 27894 geneIDs exactly match (PASS)
        Setaria_itallica                    : 35900 / 35900 geneIDs exactly match (PASS)
        Setaria_viridis                     : 35704 / 35704 geneIDs exactly match (PASS)
        Solanum_buesii                      : 43019 / 43019 geneIDs exactly match (PASS)
        Solanum_candolleanum                : 37071 / 37071 geneIDs exactly match (PASS)
        Solanum_galapagense                 : 31866 / 31866 geneIDs exactly match (PASS)
        Solanum_lycopersicum                : 46207 / 46207 geneIDs exactly match (PASS)
        Solanum_pimpinellifolium            : 34328 / 34328 geneIDs exactly match (PASS)
        Solanum_tuberosum_PG6247            : 38290 / 38290 geneIDs exactly match (PASS)
        Sorghum_bicolor_ssp.verticilliflorum: 31801 / 31801 geneIDs exactly match (PASS)
        Sorghum_bicolor                     : 31304 / 31304 geneIDs exactly match (PASS)
        Vitis_labrusca                      : 30779 / 30779 geneIDs exactly match (PASS)
        Vitis_vinifera_cultivated           : 27790 / 27790 geneIDs exactly match (PASS)
        Vitis_vinifera_ssp.sylvestris       : 38652 / 38652 geneIDs exactly match (PASS)
        Zea_luxurians                       : 72202 / 72202 geneIDs exactly match (PASS)
        Zea_mays_subsp.parviglumis          : 46218 / 46218 geneIDs exactly match (PASS)
        Zea_MaysB73                         : 41921 / 41921 geneIDs exactly match (PASS)
Checking dependencies ...
        Found valid MCScanX_h executable: `/mnt/c/Users/username/Documents/PhD/GENESPACE/apps/MCScanX/MCScanX_h`
>
>
>
> synParam <- set_syntenyParams(test)
> print(synParam$synteny$hogs)
NULL

[jtlovell]

Thanks for the help troubleshooting Noah ... I'll communicate with you via email and post a resolution here when we reach one.