Sean’s Notebook: MUMmer/nucmer error.

So I set up Metassembler to run on the BGI and Platanus assemblies to try and merge them in to a single assembly. It ran for a while, and then returned this error:

 


---------- Run bash command ----------

nucmer BGI_Plat_MetAssemb/BGI/BGI.fa BGI_Plat_MetAssemb/Platanus/Platanus.fa:
nucmer --maxmatch -l 50 -c 300 -p BGI_Plat_MetAssemb/Metassembly/QPlatanus.BGI/Q Platanus.BGI BGI_Plat_MetAssemb/BGI/BGI.fa BGI_Plat_MetAssemb/Platanus/Platanus. fa ...

1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "BGI_Plat_MetAssemb/Metassembly/QPlatanus.BGI/QPlatanus.BGI .ntref" of length 777071945
# construct suffix tree for sequence of length 777071945
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 7770719 characters per dot
/gscratch/srlab/programs/MUMmer3.23/mummer: suffix tree construction failed: tex tlen=777071945 larger than maximal textlen=536870908
ERROR: mummer and/or mgaps returned non-zero
----------------------------------------

After some googling it turns out that MUMmer naturally compiles as a 32 bit program, and since we have so much data (it ***is*** possible to have too much data) we have to recompile it in 64 bit mode to have larger intergers available to us.

Who knew.

Oh well, going to recompile and start over!

 

 

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