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

[novitch]

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.

[novitch]

Edit: I think it chomp the first letter of each directory: Error: Alignment file 1/tDNA_ND5_aa_aligned/tDNA_ND5_aa_aligned.stk doesn't exist or is not readable Could not find repository for marker tDNA_ND6_aa_aligned Could not find repository for marker tDNA_ND6_aa_aligned Could not find repository for marker tDNA_ND6_aa_aligned Error: Alignment file 1/tDNA_ND6_aa_aligned/tDNA_ND6_aa_aligned.stk doesn't exist or is not readable Could not find repository for marker tub_noOuts Could not find repository for marker tub_noOuts Could not find repository for marker tub_noOuts Error: Alignment file 1/tub_noOuts/tub_noOuts.stk doesn't exist or is not readable Could not find repository for marker tub_noOuts Could not find repository for marker tub_noOuts Could not find repository for marker tub_noOuts Error: Alignment file 1/tub_noOuts/tub_noOuts.stk doesn't exist or is not readable

Instead of those asked directories, I have in my folder: mtDNA_ND6_aa_aligned.updated: Atub_noOuts.updated: Btub_noOuts.updated:

Is it normal?

[novitch]

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