- creating co-ordinate files Failed

[sionbayliss]

- creating co-ordinate files Failed

[SionBayliss]

Hi Limin,

How were the GFF3 files created? Have the rRNA and tRNA features been annotated correctly in them?

Could you run it on a small subset of files to see if it works on only a handful?

All the best,
Sion

[limin321]

Hi Limin,

How were the GFF3 files created? Have the rRNA and tRNA features been annotated correctly in them?

Could you run it on a small subset of files to see if it works on only a handful?

All the best,
Sion

Hi Sion

I used prokka to create gff files. Here is the prokka command I used for generating gff files.

prokka --kingdom Bacteria --centre X --compliant --outdir ${base} --locustag ${base} ${dir}/${base}.fna --cpus 0 --force --prefix ${base} --addgenes

However, after I deleted -f "rRNA, tRNA"

PIRATE -i ./gff/ -o ./panOut -a -r -k "-f 6" -t 40 

PIRATE works now without -f flag. Not sure why this happens.

Thanks.

[SionBayliss]

The -f flag directs PIRATE to run on a list of features. By default the features are CDS and will be translated into amino acid sequence. If you are happy running PIRATE on CDS/gene features then the run you have started should be suitable.

By using the -f flag you directed pirate to only work on tRNA and rRNA features which would be processed as nucleotide sequence. I believe that prokka should have annotated tRNA and rRNA based upon the flags you set so I do not understand why PIRATE did not work on your files previously. I would be happy to look over a subsection of you GFF3 to work out why they didn't run with the -f flag if you would be happy to email them to me (or attach them here).

S

[limin321]

The -f flag directs PIRATE to run on a list of features. By default the features are CDS and will be translated into amino acid sequence. If you are happy running PIRATE on CDS/gene features then the run you have started should be suitable.

By using the -f flag you directed pirate to only work on tRNA and rRNA features which would be processed as nucleotide sequence. I believe that prokka should have annotated tRNA and rRNA based upon the flags you set so I do not understand why PIRATE did not work on your files previously. I would be happy to look over a subsection of you GFF3 to work out why they didn't run with the -f flag if you would be happy to email them to me (or attach them here).

S

Hi S

Thank you so much for the explaination,
I included two gff files and send them to [email protected] this email. Not sure if you can get them.
Really appreciate that you would like to test my data.

If you haven't got the gff files, please let me know, I will send again if you give me the email address.

Best,
LC

[SionBayliss]

Do you need to extract rRNA and tRNA? I didn't receive them. You can find my personal email on the PIRATE paper or just attach compressed versions here.

S

[limin321]

Do you need to extract rRNA and tRNA? I didn't receive them. You can find my personal email on the PIRATE paper or just attach compressed versions here.

S

Hi S,

Thank you so much. Yes, I am panning to look at the difference of rRNA and tRNA of different genomes. And I just sent the gff files again through the email in PIRATE paper.

Best,
LC

[SionBayliss]

Hi Limin,

I just ran PIRATE on your example files and it worked without error using:

PIRATE -i ./ -o PIRATE -f "tRNA,rRNA" -a -k '-f 6'

I installed PIRATE using conda. You may need to check it is installed correctly on your system.

S

[limin321]

Hi Limin,

I just ran PIRATE on your example files and it worked without error using:

PIRATE -i ./ -o PIRATE -f "tRNA,rRNA" -a -k '-f 6'

I installed PIRATE using conda. You may need to check it is installed correctly on your system.

S

Hi S,

Thank you so much for testing my data. I also use conda to install PIRATE.
By comparing you codes, I figured out why I failed.

your command:

PIRATE -i ./ -o PIRATE -f "tRNA,rRNA" -a -k '-f 6'

my command

PIRATE -i ./ -o PIRATE -f "tRNA, rRNA" -a -k '-f 6'

I added extra space before rRNA, leading to the error message. I didn't know the extra space will cause error.
Really appreciate that.

Best,
Limin

[SionBayliss]

Well tracked down. I will make a note to catch that in future versions!

I hope you find the software useful. Please let me know if you have any further issues.

All the best,
Sion