Error while parsing

[gubrins]

Hi all, I am really excited about using Genespace, thanks for developing this software!

I think I am having some issues regarding the parsing of my data. I tried to do it manually but it did not work, so now I am trying to use the parse_anotations function, this is my code:

genomeRepo = getwd()
wd = getwd()
path2mcscanx = "/mnt/DiscoA/cerastes/new_order/analyses/synteny/prueba/MCScanX/"
genomes2run <- c("cerastes_gasperettii", "naja_naja", "crotalus_tigris")

parsedPaths <- parse_annotations(
  rawGenomeRepo = genomeRepo,
  genomeDirs = genomes2run,
  genomeIDs = genomes2run,
  presets = "none",
  genespaceWd = wd)

And that's the output I get:

Error in setDT(ans, key = key) : 
  All elements in argument 'x' to 'setDT' must be of same length, but the profile of input lengths (length:frequency) is: [9:1, 0:8]
The first entry with fewer than 9 entries is 2
In addition: Warning message:
In setDT(ans, key = key) :
  Some columns are a multi-column type (such as a matrix column): [1]. setDT will retain these columns as-is but subsequent operations like grouping and joining may fail. Please consider as.data.table() instead which will create a new column for each embedded column.

I am not sure what is going on, I have a folder for each specific genome with each annotation in gff format and its predicted proteins, any help would be more than welcomed!

Thanks in advance!!

[jtlovell]

this is not an informative error ... I'm not sure whats up though. Can you share your genomeRepo directory? Or just post its structure and the heads of the fasta and gff3 files.

[gubrins]

Hi @jtlovell, thanks for your reply!! My directory has the three reference genomes together with a folder for each species that contains both the annotation and the proteins. Here I add a screenshot: I am not sure if this should be the proper genomeRepo directory, sorry if it is the case.

Thanks, Gabriel

[jtlovell]

Ok - yeah, this is the issue. See instructions for this here.