DeconSeq Stand Alone Project

[eprue...@gmail.com]

When I try to run the DeconSeq stand alone project eliminating bacterial data using the built in database:
perl deconseq.pl -f my_file -dbs bact
I get this error:
ERROR: cannot find all database files for database "bact" in dir "db/".

Even though when I input:
perl deconseq.pl -show_dbs
It clearly displays the bacterial database:
bact - Bacterial genomes
hsref - Human Reference GRCh37
vir - Viral genomes

Is this a bug? If not, what is the problem with my code?

[Robert Schmieder]

The show_dbs option parses the information from your config file. In order to use the databases, you need to have them downloaded to / created on your machine that is running DeconSeq.

Some of the databases are available on the FTP server. If you can't find the database you need or want a more up-to-date version, you can create your own databases following the steps outlined in the online manual (http://deconseq.sourceforge.net/manual.html#DB).

[eprue...@gmail.com]

Great thanks. Also, what are the default values for identity and coverage for the stand alone? The manual doesn't say. Or are they calculated on the go?

[Robert Schmieder]

The standalone version does not have defaults set for coverage or identidy. The thresholds should be set based on the data that is processed either with higher or lower stringency (depending on the expected similarity to the reference) or you could use the defaults from the web version that were used in the publication.

Example dataset output: http://edwards.sdsu.edu/cgi-bin/deconseq/deconseq.cgi?i=1&id=1278970172&p=1&o=1

[aliceb...@gmail.com]

Hi all,

I am getting the exact same error as above, but I have already attempted to make my own database. The only thing I can figure out is that the manual (as listed above:http://deconseq.sourceforge.net/manual.html#DB) says that the index should make 8 files, and I am only getting 5.

I'm making my own db from a bunch of combined .fasta files and this is how I have built the index:

./bwa64 index -p hsref -a div Bacterial.genomes_split_prinseq.fasta >bwa.log 2>&1 &

Have I missed a step here?

And as a separate question, I would like to also do this with the database from here: ftp://edwards.sdsu.edu:7009/deconseq/db/ but it looks like the link is broken. Will this be available again?

Thanks,
Alice

[lucilam...@gmail.com]

Hi Alice,
I am experiencing the same problem. Could you fix it?
Thank you very much.
Lucila.

[aliceb...@gmail.com]

No, I gave up! Sorry, and if you figure it out, I would still be glad to hear how.

Good luck

[lucilam...@gmail.com]

Hi! I have changed something and it seemed to work: try using -a is

That resulted in 8 files + the output.txt.

Good luck!

[insaf nasser]

hi everyone,

I have attempted all of your suggestions above and I'm still facing the same problem! any updates or new solutions that could help me with this?

thank you!