Single identifies primers beyond range

[algaraber]

Hello! I'm having a problem when running GLAPD. After running Single on a target genome, some primers generated by the program fall on positions beyond the length of the genome (if the genome is 5 040 356bp long, Single calculates primers for positions up to 5 040 965). Single runs normally, without giving any errors, but when I then try using par.pl on the results it cannot get some primers from the genome sequence using the substring command. I have also run the program with other genomes which have a single chromosome (as opposed to this one, which has one chromosome and several plasmids), and it seems to run ok.
Is this a bug or am I making some mistake running the program?

I add the commands and output below:

First, run Single:

./Single -in Aeromonas_test.fna -out Aeromonas_test

Output stream: It takes 0 seconds to prepare. There ara 6893989 candidate primers used as F3/F2/B2/B3. There are 7833456 candidate primers used as F1c/B1c. It takes 37439 seconds to identify candidate single primer regions.

Second, run par.pl:

perl par.pl \ --in Aeromonas_test \ --ref Aeromonas_test.fna \ --bowtie bowtie/bowtie \ --index indexes/Aeromonas_test_index \ --common Aeromonas_common.txt \ --left \ --threads 8

Ouput stream: Now the program is handling the 1-th file, total files is 2... In this step, it takes 5879 seconds. Now the program is handling the 2-th file, total files is 2... In this step, it takes 5589 seconds.

Error stream: substr outside of string at par.pl line 311, line 7832666. Use of uninitialized value $primer in concatenation (.) or string at par.pl line 312, line 7832666. ... Error while flushing and closing output terminate called after throwing an instance of 'int'

[jiqingxiaoxi]

Hi, algaraber! The input fasta file must have only one sequence. You can split your "Aeromonas_test.fna" file into several files, each file contains a chromosome or a plasmid.

[algaraber]

Thank you!