marker database

156 views
Skip to first unread message

ames...@googlemail.com

unread,
Dec 2, 2016, 5:54:43 AM12/2/16
to PhyloSift
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

unread,
Dec 2, 2016, 2:43:32 PM12/2/16
to phyl...@googlegroups.com
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.


--
You received this message because you are subscribed to the Google Groups "PhyloSift" group.
To unsubscribe from this group and stop receiving emails from it, send an email to phylosift+unsubscribe@googlegroups.com.
To post to this group, send email to phyl...@googlegroups.com.
Visit this group at https://groups.google.com/group/phylosift.
For more options, visit https://groups.google.com/d/optout.

ames...@googlemail.com

unread,
Dec 8, 2016, 9:00:19 AM12/8/16
to PhyloSift
thanks Guillaume,
i will download the databases and taxonmy files and see if i can get it to work that way.

ames...@googlemail.com

unread,
Dec 9, 2016, 4:51:00 AM12/9/16
to PhyloSift
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

--
You received this message because you are subscribed to the Google Groups "PhyloSift" group.
To unsubscribe from this group and stop receiving emails from it, send an email to phylosift+...@googlegroups.com.

Aaron Darling

unread,
Dec 9, 2016, 8:28:16 AM12/9/16
to PhyloSift
Hi Anthony, that message is safe to ignore.
It will be 

Aaron Darling

unread,
Dec 9, 2016, 8:29:23 AM12/9/16
to PhyloSift
oops, premature send. was typing that the message will not be produced in future phylosift releases.
Reply all
Reply to author
Forward
0 new messages