Novoindex Error

[nazebacParticipant]

Hello,
I was trying to create an index to run novoalign on a reference genome which I changed to contain ambiguous bases at variable sites (so, M,R,Y, and the like). I tried running this on an hpc cluster and the error appears basically as soon as it starts running…any help would be greatly appreciated!

Command:
novoindex name_ref_masked_IUPAC.ndx name_ref_masked_IUPAC.fasta

Error:
# novoindex (3.7) – Universal k-mer index constructor.
# Building with 13-mer and step of 2 bp.
Interrupted…11
Obtained 4 stack frames.
[0x400e76]
[0x400efc]
[0x4912bf]
[0xffffffffff600000]

[Colin HercusKeymaster]

Hi Nazebac,

Sometimes this is a build version problem. Our download page has two versions, one for Linux kernel 2.6 and one for 3.0 and later. Just check that you are not trying to run the 3.0 build on a 2.6 system.

Other than that it should be able to build with IUPAC ambiguous codes and should give meaningful errors if the input fasta file is not correctly formatted.

Could you try downloading V3.09.04 and building with the novoindex from that build. This could help as I have map files and can see from the trace which procedure it crashed in. Any index built with 3.09 can be used with 3.07.

Also, if you could share a gzipped copy of the fasta file I can take a look.

Best Regards, Colin

[Author]

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