Question: OMA error in stage 2 of 2 stage process
0
gravatar for moranr
3.1 years ago by
moranr250
Ireland
moranr250 wrote:

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

oma • 872 views
ADD COMMENTlink modified 3.1 years ago by adrian.altenhoff440 • written 3.1 years ago by moranr250
2
gravatar for adrian.altenhoff
3.1 years ago by
Switzerland
adrian.altenhoff440 wrote:

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

ADD COMMENTlink written 3.1 years ago by adrian.altenhoff440

Hi Adrain, 

No, there is no splice file. 


Thanks, 

R

ADD REPLYlink written 3.0 years ago by moranr250
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