Problem indexing , can't find repository for most of markers

39 views
Skip to first unread message

alban mathieu

unread,
Oct 9, 2018, 7:23:24 AM10/9/18
to PhyloSift
Hi,
I am trying to reinstall phylosift, i downloaded to the master repository all the files and launching phylosift does produce something (list commands available etc etc)

I downloaded the markers database and installed it on my server (can"t on my home):
/mnt/gpfs/pt2/ama/phylosift/markers/

Then I specified on phylosiftrc where is my db and ncbi file:

 43 $marker_dir="/mnt/gpfs/pt2/ama/phylosift/markers/";
 44 # $markers_extended_dir="";
 45 $ncbi_dir = "/mnt/gpfs/pt2/ama/phylosift/ncbi/";


When i launch the index ./phylosift index --config phylosiftrc

Here is a snapshot of the stdout:
Could not find repository for marker 0S
Could not find repository for marker 0S
Could not find repository for marker 0S
Could not find repository for marker 0S
1/0S/0S.rep not found.
Warning: marker 0S appears to be missing data
Could not find repository for marker 4_3_3
Could not find repository for marker 4_3_3
Could not find repository for marker 4_3_3
Could not find repository for marker 4_3_3
1/4_3_3/4_3_3.rep not found.
Warning: marker 4_3_3 appears to be missing data
Could not find repository for marker 5
Could not find repository for marker 5
Could not find repository for marker 5
Could not find repository for marker 5


I don't understand the repositories that it tries to open because the 1/ directory doesn't exist :
for instance here I have the 14_3_3/ but not the 1/4_3_3/


Is there any bug in what I did?

Thanks,

Alban.

alban mathieu

unread,
Oct 9, 2018, 9:06:09 AM10/9/18
to PhyloSift
ok, I had a "/" at the end of my folders at the end that chomp the first letters

It works with this:
43 $marker_dir="/phylosift/markers";
44 # $markers_extended_dir="";
45 $ncbi_dir = "phylosift/ncbi";

Guillaume Jospin

unread,
Oct 9, 2018, 9:07:19 AM10/9/18
to phyl...@googlegroups.com
Hi Alban,
Can you try removing the last / from the paths in your phylosiftrc file?
Shouldn’t be an issue but I think the path manipulation might get screwed up because of it. 

Sent from my iPhone
--
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.
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.

Guillaume Jospin

unread,
Oct 9, 2018, 9:08:48 AM10/9/18
to phyl...@googlegroups.com
Looks like you fixed your problem anyways. Thanks for passing the solution along!


Sent from my iPhone

alban mathieu

unread,
Oct 9, 2018, 9:17:46 AM10/9/18
to PhyloSift
Yes that was the solution, sorry to pollutate gihub/google groups :)

Anyway thanks for your quick answer,

Alban.
Reply all
Reply to author
Forward
0 new messages