marker database

[ames...@googlemail.com]

Afternoon,

I am attempting to run phylosift but am running into a few errors.

When investigating things it appears that when I download Phylosift it didn't include the marker database.  I have tried to download and install the program again and also rebuild the database but I have been unsuccessful.

Could you please on the best way to obtain the marker database so that i can run the program.

Many thanks,
Anthony

[Guillaume Jospin]

Hello Anthony,

You could try manually downloading the marker database from http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift_markers/markers.tgz

and the ncbi taxonomy used by PS from http://edhar.genomecenter.ucdavis.edu/~koadman/ncbi.tgz

The software will look for the DB at the following path ~/share/phylosift as default. You can modify this in the phylosiftrc file if needed.

What kind of error are you seeing when it is failing to download the database? I am wondering if our firewalls have been modified to block an automatic download.

I hope this helps, let me know if you have any more questions.

Guillaume.

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[ames...@googlemail.com]

thanks Guillaume,
i will download the databases and taxonmy files and see if i can get it to work that way.

[ames...@googlemail.com]

I have downloaded the marker and ncbi directories and attempted to run PS but am getting a new error message
rm: cannot remove '/home/.../phylosift/test/blastDir/*.aa.1*': No such file or directory
Any advice would be gratefully received in resolving this.

On Friday, 2 December 2016 19:43:32 UTC, Guillaume Jospin wrote:

Hello Anthony,

You could try manually downloading the marker database from http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift_markers/markers.tgz

and the ncbi taxonomy used by PS from http://edhar.genomecenter.ucdavis.edu/~koadman/ncbi.tgz

The software will look for the DB at the following path ~/share/phylosift as default. You can modify this in the phylosiftrc file if needed.

What kind of error are you seeing when it is failing to download the database? I am wondering if our firewalls have been modified to block an automatic download.

I hope this helps, let me know if you have any more questions.

Guillaume.

On Fri, Dec 2, 2016 at 2:54 AM, amesser81 via PhyloSift <phyl...@googlegroups.com> wrote:

Afternoon,

I am attempting to run phylosift but am running into a few errors.

When investigating things it appears that when I download Phylosift it didn't include the marker database.  I have tried to download and install the program again and also rebuild the database but I have been unsuccessful.

Could you please on the best way to obtain the marker database so that i can run the program.

Many thanks,
Anthony

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To unsubscribe from this group and stop receiving emails from it, send an email to phylosift+...@googlegroups.com.

[Aaron Darling]

Hi Anthony, that message is safe to ignore.

It will be 

[Aaron Darling]

oops, premature send. was typing that the message will not be produced in future phylosift releases.