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jtlovell / GENESPACE

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Stuck at step 3. #98

Closed theo-allnutt-bioinformatics closed 1 year ago

theo-allnutt-bioinformatics commented 1 year ago

My run seems to hang at step 3. No files updated in results/ for 2.5 hours..

  1. Combining and annotating the blast files with orthogroup info ...

    Chunk 1 / 1 (13:46:59) ...

Using latest version. Script:

library(GENESPACE)

wd <-"/g/data/nm31/d/r17_nepenthes/r17.2_synteny/gs2/"

path2mcscanx <- "/g/data/nm31/bin/MCScanX/"

genomes2run <- c("nm","ft","bv","so")

gpar <- init_genespace(
  genomeIDs = genomes2run,
  wd = wd,
  nCores = 48,
  blkSize=3,
  onlyOgAnchors=F,
  nSecondHits=10,
  path2mcscanx = path2mcscanx)

out <- run_genespace(gpar, overwrite = T)
theo-allnutt-bioinformatics commented 1 year ago

genespace.zip data

jtlovell commented 1 year ago

Those are some strange parameters. Does it run without all that and nCores = 1?

jtlovell commented 1 year ago

I just pushed it through with defaults without a problem. But these genomes look pretty problematic and you may want to do some QC first ... For example, bv has a huge bottom drawer and a huge amount of off-diagonal orthogroup hits. nm has two scaffolds that are entirely a single array and essentially no synteny, so is not scaffolded and is probably too split up for synteny to be useful.

theo-allnutt-bioinformatics commented 1 year ago

It's a fringe case. Yes it worked on a PBS job in ~2 hours. I think it was throttled previously and couldn't close a thread.