How to fix Prokka`s annotation software error?

Question

[bioinformatics_bel]

How to fix Prokka`s annotation software error:

./prokka.sh <file_name.fasta>

it returns:

[15:27:44] Using genetic code table 11. [15:27:44] Loading and checking input file: FastaSequences.fasta [15:27:44] Uh oh! Sequence file 'FastaSequences.fasta' contains duplicate sequence ID: SRR1181196.1

I have tried BBMap`s dedupe.sh in=FastaSequences.fasta am=f ac=f fo c pc rnc=f mcs=4 mo=100 s=1 pto cc qin=33 csf=stats.txt pattern=cluster_%.fasta dot=graph.dot out=result.fa

and it finds no duplicates

What to do to get an annotation files from Prokka?

[Matt Shirley]

Maybe post a bit of your file or the output from grep -A1 SRR1181196.1 FastaSequences.fasta

[Matt Shirley]

Maybe post a bit of your file or the output from grep -A1 SRR1181196.1 FastaSequences.fasta

[GenoMax]

Did you get this data from SRA? Appears that you must not have used the option to retrieve the original Illumina format fastq read headers. You could get the fastq files directly from EBI-ENA and use those with prokka.

Answer 1

[Matt Shirley]

Maybe post a bit of your file or the output from grep -A1 SRR1181196.1 FastaSequences.fasta

[Istvan Albert]

just testing comments on this thread according to issue:

https://github.com/ialbert/biostar-central/issues/444

[aswathyseb]

this is a tests as per:

https://github.com/ialbert/biostar-central/issues/444