ERROR: Query input does not match delta file

[yhsYhsYhs]

hello, Could u help me why this appered?thanks

thinkstation# dnadiff sequence.fasta query.fasta Building alignments Filtering alignments Extracting alignment coordinates Analyzing SNPs ERROR: Query input does not match delta file ERROR: Failed to run show-snps, aborting.

[ajuric]

I also have the same problem.

Any help?

[ajuric]

This was my problem, I hope it helps someone:

Query file (in my case .fasta file), which is second input in dnadiff, had multiple contigs and all those contigs had the same name.

After giving all contigs unique names, dnadiff is working normally.

Please, fix this or give appropriate error message: https://github.com/garviz/MUMmer/blob/master/src/tigr/delta.cc#L1286

[andrewrobertjones]

I had the same error message with show-snps (but other nucmer tools worked okay). In my case, my fasta files had Windows end of line chars. The problem went away when I converted fasta end of lines on input and query to Linux.

[pks16]

I too had this error while running "show-snps" and checked input file which was fine. Nothing wrong with the input file then why the error was showing? The actual issue was input file that is not in unix end of line format. Thus coversion from windows end of line (CRLF) to unix end of line (LF) format can be done by using "tr -d '\15\32'< windows_format.fasta > unix_format.fasta" in a bash terminal.

[2iut128374gb21563]

Duplicate of #70 I suggested another possible solution to the error there, maybe it helps!