OMA error in stage 2 of 2 stage process

Question

[moranr]

Hi,

I get the following when trying to run the second stage of OMA on a test batch:

Reading the all-against-all files...

# 5kGenes_Ancylostoma_ceylanicum vs 5kGenes_Ancylostoma_ceylanicum done, (5178/5178)
# 5kGenes_Ancylostoma_ceylanicum vs AEDAE done, (2941/2941)
# 5kGenes_Ancylostoma_ceylanicum vs MOUSE done, (5324/5324)
# AEDAE vs AEDAE done, (62332/62332)
# AEDAE vs MOUSE done, (74258/74258)
# MOUSE vs MOUSE done, (769460/769460)
# Matches loaded. Mem: 0.541GB
minus expects a 1st argument, a:{set,identical(intersect())}, found: [3, 4]
Error, (in FilterBestSplicingMatches) invalid arguments

What is this error ?

Thanks,
R

Answer 1

[Adrian Altenhoff]

Hi Ray,

this error looks like the format of the splicing variants is somehow screwed up. From the first look at it, it seems that the extracted gene/protein mapping contains some unexpected types. Just to verify: Did you provide a spliceing file for 5kGenes_Ancylostoma_ceylanicum, e.g. a file DB/5kGenes_Ancylostoma_ceylanicum.splice?

I opened an issue for this and will keep you posted.

Best wishes

Adrian

[moranr]

Hi Adrain,

No, there is no splice file.

Thanks,

R