Failing to cluster (_cluster_analysis.pl)

[SamCT]

Hello,

I am trying to troubleshoot an issue with the clustering, wherein my result is core genes = 0 out of ~150,000 genes.

`# /hpc/get_pangenes-20240627/plant-scripts/pangenes/cluster_analysis.pl -r Genomes_Final -f /hpc/pangenes/Genomes2_pangenes/Genomes_Final_0taxa_5neigh_algMmap -g 0 -S 0 -m 5 -v 1 -t 0 -x -p 0 -R 12345 -B bedtools

-T /hpc/pangenes/Genomes2_pangenes/tmp/mergedpairs.tsv`

'# parsing TSV files

WARN: skip gene model Genome1_Final Genome1_g1000^M as it lacks cDNA (no coordinates)

WARN: skip gene model Genome1_Final Genome1_g10000^M as it lacks cDNA (no coordinates)'

and

`# Genome1_Final : sequences = 33018 clusters = 32577 (unclustered = 317 , singletons = 4638)

Genome2_Final : sequences = 34704 clusters = 34293 (unclustered = 207 , singletons = 6158)

Genome3_Final : sequences = 40863 clusters = 40536 (unclustered = 56 , singletons = 17256)

Genome4_Final : sequences = 42274 clusters = 42274 (unclustered = 0 , singletons = 42274)

total sequences = 150859

number of clusters = 99689 (core = 0)`

In the troubleshooting section it says to rerun the command locally, but I am getting the same error. How should I approach this issue?

Thanks,
Sam