I have received this message recently while using makeblastdb for rmblast in RepeatMasker, and it is a real head-scratcher for me.
After no errors and completely running through all cycles, RepeatMasker finishes but there are no output files. The only trace of the analysis is the rmblastdb.log file in the RepeatMasker/Libraries directory which reads:
Building a new DB, current time: 05/29/2014 10:54:02 New DB name: /home/mtollis/RepeatMasker/Libraries/20140131/anolis/specieslib New DB title: /home/mtollis/RepeatMasker/Libraries/20140131/anolis/specieslib Sequence type: Nucleotide Keep Linkouts: T Keep MBits: T Maximum file size: 1000000000B Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 100% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 100% ambiguous nucleotides (shouldn't be over 40%) Adding sequences from FASTA; added 776 sequences in 0.108892 seconds.
Perhaps the makeblastdb "error" is harmless and maybe it is merely coincidental that my analysis fails. I don't see how either true ambiguities or line endings are the problem, as my database is hardly novel: I am using the RepBase update and the -species command. the command appears to work, as it creates the species specific library as well as the general library in the RepeatMasker/Libraries directory.
Does anyone know why RepeatMasker would run without throwing any errors and then leave no output files whatsoever?