Error when analysing a sequence

[thorcs1]

Hello,

I recently found your tool, which I find quite interesting. I was trying it with some Vibrio vulnificus genomes, and it worked perfectly. However, for two strains, it retrieved an error that I do not understand, and I would like to know if you could help me with that.

Genomes were annotated with Bakta 1.11.3 and when I ran the command:
StORF-Reporter -anno Bakta Out_Dir -p /Alb2_bakta/ -af Alb2 -odir Alb2_bakta/

I get the following error:
No URs in seq (repeated several times)
No URs in seq
No URs in seq
No URs in seq
Error: Original seq GCBPMDJBDG_158_repeat_1 not found

I attached the fna and gff3 files from Bakta to see if you could shed some light on the matter. Thank you in advance!

Alb2.fna.txt
Alb2.gff3.txt

[NickJD]

Hi @thorcs1 - Glad StORF-Reporter is mostly working for you.
I think the problem was with how it expects the Bakta/Prokka files to be presented, as it wants to read in the .faa and .fnn files but you only provided it with the .fna file.
Really it shouldn't need those files as we can compute what we need from just the .fna and .gff so I have now modified the code accordingly.
I have also silenced the No URs in seq printout, but as with all the logging information, it can be added back with -verbose.

The new version - 1.4.6 - Is now available via pip and has a new release on GitHub https://github.com/NickJD/StORF-Reporter/releases/tag/v1.4.6

Let me know how it works for you.

[thorcs1]

Yes! Now it works perfectly fine. Thank you very much for your quick response.

[thorcs1]

Hello! Sorry for bothering you again.
I tried to run Panaroo after annotating with StORF-Reporter and had an error of duplicated entries. For some strains, there are duplicated entries in the resulting gff.
For instance, in the attached file, in the resulting gff, these entries are repeated with different names:
contig_77 StORF-Reporter CDS 655 774 . + 0 ID=StORF_14a103c9fbfebce5;locus_tag=contig_77_UR_604_786_StORF_0;INFO=Additional_Annotation_StORF-Reporter;UR_Stop_Locations=47-170;Name=StORF_3511;StORF_Num_In_UR=0;StORF_Length=120;StORF_Frame=1;UR_StORF_Frame=3;Start_Stop=TAA;Mid_Stops=N/A;End_Stop=TAA;StORF_Type=StORF
contig_77 StORF-Reporter CDS 655 774 . + 0 ID=StORF_d979ba90003155a6;locus_tag=contig_78_UR_604_786_StORF_0;INFO=Additional_Annotation_StORF-Reporter;UR_Stop_Locations=47-170;Name=StORF_3512;StORF_Num_In_UR=0;StORF_Length=120;StORF_Frame=1;UR_StORF_Frame=3;Start_Stop=TAA;Mid_Stops=N/A;End_Stop=TAA;StORF_Type=StORF

contig_71 StORF-Reporter CDS 893 1012 . - 0 ID=StORF_26adc76491ef67fc;locus_tag=contig_71_UR_891_1047_StORF_0;INFO=Additional_Annotation_StORF-Reporter;UR_Stop_Locations=4-127;Name=StORF_3502;StORF_Num_In_UR=0;StORF_Length=120;StORF_Frame=5;UR_StORF_Frame=6;Start_Stop=TGA;Mid_Stops=N/A;End_Stop=TAG;StORF_Type=StORF
##sequence-region contig_72 1 1019
contig_72 Bakta region 1 1019 . + . ID=contig_72;Name=contig_72
contig_71 StORF-Reporter CDS 893 1012 . - 0 ID=StORF_b73ee68f70bee8a8;locus_tag=contig_72_UR_891_1047_StORF_0;INFO=Additional_Annotation_StORF-Reporter;UR_Stop_Locations=4-127;Name=StORF_3503;StORF_Num_In_UR=0;StORF_Length=120;StORF_Frame=5;UR_StORF_Frame=6;Start_Stop=TGA;Mid_Stops=N/A;End_Stop=TAG;StORF_Type=StORF

Permar1.tar.gz

[NickJD]

Hi @thorcs1 - That is a strange one!
Can you reply with the exact parameters you used.
I think I know what the problem is but just need to double check.

Thanks.

[thorcs1]

Sure! I used the default paramaters. I ran a for loop to annotate all genomes.

for d in *_bakta/; do dc="${d%/}"; id="${dc%_bakta}"; StORF-Reporter -anno Bakta Out_Dir -p "$d" -af "$id" -odir "$d" -overwrite; done

Then, in case it was some kind of problem with the loop I ran the command exclusive to this strain:

StORF-Reporter -anno Bakta Out_Dir -p Permar1_bakta/ -af Permar1 -odir Permar1 -overwrite

In both cases the outcome was the same.

[NickJD]

Try updating to v1.4.7 and let me know how you get on.
I have tested on the files you provided and it seems to be working now.

[thorcs1]

Indeed! With the new version I do not have duplicated sequences and I could run Panaroo. I hope in the future this tool is implemented in annotators such as Bakta, I think it would enrich databases. Thank you again!