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

[alban mathieu]

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]

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]

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

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[Guillaume Jospin]

Looks like you fixed your problem anyways. Thanks for passing the solution along!

Sent from my iPhone

[alban mathieu]

Yes that was the solution, sorry to pollutate gihub/google groups :)

Anyway thanks for your quick answer,

Alban.