primersearch Illegal character '/' error: EMBOSS An error in primersearch.c at line 499
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23 months ago

I am trying to run primersearch to get a large batch of primer pairs against a directory of around 45 fasta files. When I try to run it for one using the command below, I get the error that follows. I also have the debug file, but I don't know how to upload that. I've tried with EMBOSS/6.5.7 and EMBOSS/6.4.0. Has anyone seen this error, or at least have a clue what it means?

primersearch -seqall sequences/SAMN04014954.fasta -infile primerList.txt -mismatchpercent 10 -outfile SAMN04014954

Search DNA sequences for matches with primer pairs
Warning: Illegal character '/'
EMBOSS An error in primersearch.c at line 499:
Illegal pattern


primersearch emboss error warning • 554 views
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Did you search the fasta file for any instances of /? eg:

grep -n "/" SAMN04014954.fasta


This will give you line number as well. Check both your files.

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Thanks! I had checked that. I figured out that the problem was with my primer file - basically I had two, each formatted differently for different purposes, and I was calling the wrong one. Stupid mistake. Still, that was a strange error...would been a lot easier to troubleshoot the problem if there were some kind of formatting check on the files that issued a human-readable message like, "Invalid file format".

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Totally agree but error checking is a never ending issue :) Glad you figured it out.