ProDeGe JGI. Installation Error

Question

[celine.petitjean]

Dear Biostar community,

I would like to use the software ProDeGe on one of my assembly, and I have a reccurent error when I am installing it: I tried to install ProDeGe on the unix (central OS) cluster I am working on and on my macpro but I have recurrent errors and the installation is unsuccessful. The errors seems to come from blast and from R, but they are both installed in the cluster. I copy bellow the errors lines and the versions of the required software.

I can't figure out how to solve this problem. Would anyone is using ProDeGe or would have an idea on how to solve this problem?

Thank you in any case!!

Here are the installed versions of the required softwares:

Blastn: version Nucleotide-Nucleotide BLAST 2.6.0+ perl 5, version 16, subversion 3 (v5.16.3) Bio::SeqIO and Bio::Perl should been installed PRODIGAL v2.6.3 [February, 2016] R version 3.4.1 (2017-06-30) -- "Single Candle"

Here are the last lines of the installation process:

Building a new DB, current time: 09/27/2017 19:09:19 New DB name: /home/cp16344/bin/NCBI-nt-euk/nt_euks New DB title: nt_euks.fna Sequence type: Nucleotide Deleted existing Nucleotide BLAST database named /home/cp16344/bin/NCBI-nt-euk/nt_euks Keep MBits: T Maximum file size: 1000000000B BLAST options error: File nt_euks.fna does not exist rm: cannot remove ‘nt_euks.fna’: No such file or directory

Building a new DB, current time: 09/27/2017 19:09:24 New DB name: /home/cp16344/bin/IMG-db/imgdb New DB title: imgdb.fna Sequence type: Nucleotide Deleted existing Nucleotide BLAST database named /home/cp16344/bin/IMG-db/imgdb Keep MBits: T Maximum file size: 1000000000B BLAST options error: File imgdb.fna does not exist rm: cannot remove ‘imgdb.fna’: No such file or directory R packages not installed. ProDeGe installation unsuccessful.

[Brian Bushnell]

It looks like the problem is that you are missing imgdb.fna, but I don't know how you'd get that; JGI does not provide IMG as a single file and there is no convenient way to download all of it.

[celine.petitjean]

Hi Brian,

Thank you very much for your answer, I have just seen it! Did you already worked with ProDeGe?

Thank you again?

[Brian Bushnell]

I work at JGI, so I am familiar with IMG and aware of ProDeGe, but I don't personally use it. It still runs as part of some of our automated pipelines for identifying possible contaminants, but it is no longer actively developed or maintained.

[liangdong0309]

Hi, Barian, Would u mind sending me the pipelines of ProDeGe? I tried my best to find it but I failed.my email address is [e-mail] Thank u very much

[GenoMax]

Looks like ProDeGe can be found on this page.