Question: How to fix Prokka`s annotation software error?
0
gravatar for bioinformatics_bel
2.3 years ago by
US, Alaska
bioinformatics_bel20 wrote:

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?

ADD COMMENTlink modified 2.3 years ago by Matt Shirley9.2k • written 2.3 years ago by bioinformatics_bel20

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

ADD REPLYlink written 2.3 years ago by Matt Shirley9.2k

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

ADD REPLYlink written 2.3 years ago by Matt Shirley9.2k

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.

ADD REPLYlink written 2.3 years ago by genomax77k
0
gravatar for Matt Shirley
2.3 years ago by
Matt Shirley9.2k
Cambridge, MA
Matt Shirley9.2k wrote:

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

ADD COMMENTlink written 2.3 years ago by Matt Shirley9.2k

just testing comments on this thread according to issue:

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

ADD REPLYlink written 2.2 years ago by Istvan Albert ♦♦ 82k

this is a tests as per:

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

ADD REPLYlink written 2.2 years ago by aswathyseb30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2183 users visited in the last hour