Error in step 3 - Githubissues

Hi all, I am excited about working with Genespace, thanks for developing this package! I am trying to run genespace on several genomes, but I cannot proceed further than step 3, this is the code I used:

library(GENESPACE)
wd = "/mnt/DiscoA/cerastes/new_order/analyses/synteny/prueba"
path2mcscanx = "/mnt/DiscoA/cerastes/new_order/analyses/synteny/prueba/MCScanX/"

genomes2run <- c("cro_tigris","cerastes","naja")

gpar <- init_genespace(
  wd = "/mnt/DiscoA/cerastes/new_order/analyses/synteny/prueba/results_orthofinder", 
  path2mcscanx = "/mnt/DiscoA/cerastes/new_order/analyses/synteny/prueba/MCScanX/")
gpar <- run_genespace(gsParam = gpar)

And this is the output:

############################
1. Running orthofinder (or parsing existing results)
    Checking for existing orthofinder results ...
[1] FALSE
    ... found existing run, not re-running orthofinder
        re-ordering genomeIDs by the species tree: crotalus_tigris,
                cerastes_gasperettii, naja

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

############################
3. Combining and annotating the blast files with orthogroup info ...
    # Chunk 1 / 1 (14:28:38) ... 
Error in rbindlist(mclapply(1:nrow(chnk), mc.cores = nCores, function(i) { : 
  Item 2 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) { :
  scheduled cores 6, 5, 4, 2, 3 encountered errors in user code, all values of the jobs will be affected

I have seen several posts saying that changing the number of cores in init_genespace to 1 should work or that reinstalling the package data.table should fix it, but it did nor work.

I have my data in the working directory within two different folders: bed and peptide.

This is heads on the peptide file:

>XM_039321119.1
METEASQPGLASPDSPHDPCKMFIGGLSWQTTQEGLREYFSQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQPKEVMSPTGSARGRSRVMPYGMDAFMLGIGMLGYPGFQAATYTSRSYTSIAPGYTYQFPEFRVERTPLPSAPVLSELTAIPLTAYGPMAAAAAAAVVRGTGSTPSRTGGFLGTTSPGPMAELYGAANQDSGVSSYISAASPAPSTGFGHSLGGPLIATAFTNGYH*
>XM_039333404.1
MQAREREAKQARACGGVSREARRSPAQQAGAGVRPRGMESLLENPVRAVLYLKELTAIVQNQQSLIHTQRQRIDELEKRLDELSTENRSLREQYALPAETPPPLQPRVPPAASLPCRAPPQGQQQPPLAAAAQQEEFQHHQQLPALQPPPPPRQPPPPPPPSSSKQAQAGPSGTRTPVSHQHPSLQPHQHHHEDSREKSCCPALLQHKSPPALGKGVLVRRLENETVLHQFCCPAADAEQKPSSADSSSSDDPCGSASKKTGCDVEEPKESGRGSGQEGRSDTLKLKAQHEERQEEQAAGSSLLVQKASLHHTGSPVRGQRSKGAATCSHAAASNYELSLDLKNKQIEMLEHKYGGHLVSRRAACTIQTAFRQYQLSKNFEKIRNSLLESRMPRRISLRTLRVQNSENFSAEKALVEGYNFVGIPLVRSPSLPVTISGALTELEDSFTEQVQSLAKSIDDALSTWSLKTMCSLQDGSSYQIRETFSTSSMQPNQDLDMELKEQEKEEGLLPDTLPKSSSTLMMAFRDVTVQIDNKNISVSSSTSVSMANCLANSSQAGISSAAKIEEIPVEGEKEDKDLQVVSEGQPDAGALQNSHPVTEANLNTNGLEKGEAEQDQMMMPKLDFGSENGTGQHKGSEAENVDNLEQLSSSSTSTSAKSASELSSKEALQAMILSLPRYHCENPAVCKSPTLSTDTMRKRLYRIGLNLFNINPDKGIQFLISRGFIPDTPIGVAHFLLQRKGLSRQMIGEFLGNSKKQFNRDVLDCVVDEMDFSGMELDEALRKFQAHIRVQGEAQKVERLIEAFSQRYCMCNPDVVQQFHNPDTIFILAFAIILLNTDMYSPNIKPDRKMMLEDFIRNLRGVDDGADIPRDLVVGIYERIQQRELKSNEDHVTYVTKVEKSIVGMKTVLSVPHRRLVCCSRLYEVTDVNKVQKHAAHQREVFLFNDLLVILKLCPKKKSSSTYTFCKSVGLLGMQFHLFENEYYPHGITLVIPVSGSEKKQVLHFCALNAEEMQKFVEDLKESIAEVMELEQIRIECKTPSVFQTPCSHSVWELEKQHGAKNLSLKTNGAQMEMQYKQGSPAGKKDLGEKGPENTVEVLINASPARLTILPISRDTIKSYC*

And this for the bed file:

NW_024096460.1  201971  240245  XM_039352218.1
NW_024096460.1  210756  240245  XM_039352373.1
NW_024096460.1  218782  240245  XM_039352288.1
NW_024096460.1  248986  276964  XM_039336548.1
NW_024096460.1  283300  296042  XM_039352494.1
NW_024096460.1  297063  344309  XM_039351202.1
NW_024096460.1  399013  429483  XM_039322463.1
NW_024096460.1  399013  429483  XM_039349243.1
NW_024096460.1  399013  429483  XM_039357611.1
NW_024096460.1  399013  429483  XM_039365935.1

Any thoughts about what is going on? Thanks in advance!!!

jtlovell / GENESPACE

Error in step 3 #125