Error when running run_genespace

[topa92]

Hello,
I'm having the following error when running genespace:

out <- run_genespace(gpar,overwrite = TRUE)

############################

1. Running orthofinder (or parsing existing results)
   Checking for existing orthofinder results ...
   [1] FALSE
   ... found existing run, not re-running orthofinder

############################
2. Combining and annotating bed files w/ OGs and tandem array info
...
##############
Flagging chrs. w/ < 10 unique orthogroups
...Carve_hap1: 3 genes on 1 small chrs.
...Carve_hap2: 0 genes on 0 small chrs.
##############
Flagging over-dispered OGs
...Carve_hap1: 1880 genes in 70 OGs hit > 8 unique places
...Carve_hap2: 2407 genes in 105 OGs hit > 8 unique places ***
NOTE! Genomes flagged *** have > 5% of genes in
over-dispersed orthogroups. These are likely not
great annotations, or the synteny run contains
un-specified WGDs. Regardless, these should be
examined carefully
##############
Annotation summaries (after exclusions):
...Carve_hap1: 37636 genes in 30517 OGs || 4882 genes in 1591 arrays
...Carve_hap2: 35582 genes in 30284 OGs || 4289 genes in 1418 arrays

############################
3. Combining and annotating the blast files with orthogroup info ...
# Chunk 1 / 1 (14:17:21) ...
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
In addition: Warning message:
In mclapply(1:nrow(chnk), mc.cores = nCores, function(i) { :
all scheduled cores encountered errors in user code

What could be going wrong?

Thank you for your time,
Best
-Sofia

[jtlovell]

Hard to say ... try running with nCores = 1 and it will return a more informative error.
This is the kind of error that occurs when you don't have synteny or all genes are on small scaffolds. Are either of those possible?

[topa92]

Hi, sorry for the delay in getting back to this issue.
It's a phased de novo assembly and I'm trying to compare both haplotypes.
Annotation looks good spanning through all chromosomes.

[goshng]

Hard to say ... try running with nCores = 1 and it will return a more informative error. This is the kind of error that occurs when you don't have synteny or all genes are on small scaffolds. Are either of those possible?

with nCores=1 options in init_genespace function, I have a different error message: Thank you!

############################
2. Annotated/concatenated bed file exists

############################
3. Combining and annotating the blast files with orthogroup info ...
Error in fwrite(x, file = filepath, showProgress = F, quote = F, sep = "\t") :
  Compression in fwrite uses zlib library. Its header files were not found at the time data.table was compiled. To enable fwrite compression, please reinstall data.table and study the output for further guidance.

[goshng]

I had that error when using the test data. The following is a related link to that error. Thank you!

#148 (comment)

[topa92]

I tried with the ncore=1 and now I'm having the same error as goshng.
Any news on how to fix it?

[DrPintoThe2nd]

Hi, running into the same issue. Any word on this @jtlovell ?

[jtlovell]

I have recreated the error and am troubleshooting. More soon

[xiaoguizz]

Hello, I'm having the following error when running genespace:

out <- run_genespace(gpar,overwrite = TRUE)

############################

1. Running orthofinder (or parsing existing results)
   Checking for existing orthofinder results ...
   [1] FALSE
   ... found existing run, not re-running orthofinder

############################ 2. Combining and annotating bed files w/ OGs and tandem array info ... ############## Flagging chrs. w/ < 10 unique orthogroups ...Carve_hap1: 3 genes on 1 small chrs. ...Carve_hap2: 0 genes on 0 small chrs. ############## Flagging over-dispered OGs ...Carve_hap1: 1880 genes in 70 OGs hit > 8 unique places ...Carve_hap2: 2407 genes in 105 OGs hit > 8 unique places *** NOTE! Genomes flagged *** have > 5% of genes in over-dispersed orthogroups. These are likely not great annotations, or the synteny run contains un-specified WGDs. Regardless, these should be examined carefully ############## Annotation summaries (after exclusions): ...Carve_hap1: 37636 genes in 30517 OGs || 4882 genes in 1591 arrays ...Carve_hap2: 35582 genes in 30284 OGs || 4289 genes in 1418 arrays

############################ 3. Combining and annotating the blast files with orthogroup info ... # Chunk 1 / 1 (14:17:21) ... 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 In addition: Warning message: In mclapply(1:nrow(chnk), mc.cores = nCores, function(i) { : all scheduled cores encountered errors in user code

What could be going wrong?

Thank you for your time, Best -Sofia

Hello, I'm having the following error when running genespace:

out <- run_genespace(gpar,overwrite = TRUE)

############################

1. Running orthofinder (or parsing existing results)
   Checking for existing orthofinder results ...
   [1] FALSE
   ... found existing run, not re-running orthofinder

############################ 2. Combining and annotating bed files w/ OGs and tandem array info ... ############## Flagging chrs. w/ < 10 unique orthogroups ...Carve_hap1: 3 genes on 1 small chrs. ...Carve_hap2: 0 genes on 0 small chrs. ############## Flagging over-dispered OGs ...Carve_hap1: 1880 genes in 70 OGs hit > 8 unique places ...Carve_hap2: 2407 genes in 105 OGs hit > 8 unique places *** NOTE! Genomes flagged *** have > 5% of genes in over-dispersed orthogroups. These are likely not great annotations, or the synteny run contains un-specified WGDs. Regardless, these should be examined carefully ############## Annotation summaries (after exclusions): ...Carve_hap1: 37636 genes in 30517 OGs || 4882 genes in 1591 arrays ...Carve_hap2: 35582 genes in 30284 OGs || 4289 genes in 1418 arrays

############################ 3. Combining and annotating the blast files with orthogroup info ... # Chunk 1 / 1 (14:17:21) ... 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 In addition: Warning message: In mclapply(1:nrow(chnk), mc.cores = nCores, function(i) { : all scheduled cores encountered errors in user code

What could be going wrong?

Thank you for your time, Best -Sofia

Hello,
How to run Genescape when you already have an OrthoFinder result file?
Thouk you,
Zhou

[ferrojm]

Hi!

I have encountered the same issue. Is there any update on this or an alternative workaround (e.g., removing some annotations)?

To provide further context, in my case, there is a disproportionate difference in protein numbers between the two species I am trying to analyze. Genespace ran smoothly when comparing two samples of the same species, but now I am stuck.

Cheers,
Juan