Open Hannah1746 opened 1 month ago
Please try running with nCores = 1 and reporting the error. Usually this happens when there is no synteny, but there are other possible causes.
Here is the new error: ############################
wd = "/mnt/krab3/catostomid_GENESPACE" setwd(wd)
path2mcscanx <- "/home/krablab/Documents/apps/MCScanX"
gpar <- init_genespace( wd = wd, path2mcscanx = path2mcscanx, genomeIDs = c("DR","M.asiaticus", "X.texanus", "H.nigricans","C.commersonii", "M.valenciennesi"), ploidy = c(0,1,1,1,1,1), nCores = 1 )
out <- run_genespace(gpar, overwrite = T)
I never thought to check for ploidy > 0 ... can you try that, ploidy = c(0,1,1,1,1,1) + 1
So this moved me forward but I am still getting an error:
The thing is I have used the bed and fasta before to plot and it work but now it is not working. When I take it out I can also get it to run.
I am sorry for taking up so much of your time!!!
Its alright ... how do the dotplots look? Is it possible there is no synteny?
No there is synteny. All the dotplots show that. Here are a couple of them: Drer_vs_Gyro.syntenicHits.pdf Drer_vs_H.nigricans.syntenicHits.pdf X.texanus_vs_Drer.syntenicHits.pdf X.texanus_vs_Gyro.syntenicHits.pdf
pls send me an email so I can troubleshoot your run. jlovell [at] hudsonalpha [dot] org
OK - there is something funky with your run that was causing there to be duplicated block coordinates ... I couldn't figure out what was causing that, but I did just commit a change to master that now runs through your genomes without erroring out.
I am running GENESPACE and keep running into this error and I can't seem to pin down what is causing the error.
############################
Chunk 1 / 2 (02:10:40 PM) ...
Error in rbindlist(mclapply(1:nrow(chnk), mc.cores = nCores, function(i) { : Item 1 of input is not a data.frame, data.table or list Calls: run_genespace -> synteny -> rbindlist -> lapply -> FUN -> rbindlist In addition: Warning message: In mclapply(1:nrow(chnk), mc.cores = nCores, function(i) { : scheduled core 1 encountered error in user code, all values of the job will be affected Execution halted
I know what individual is causing the problem but the bed and protein fasta inputs don't seem to have anything wrong with them.
I would love some help trying to debug this if you have time.