Hi Dan,
Thanks for the solution! It did help me to identify a missing index
file. I think the indexing run of that particular config maf file
failed for some reason. Since I don't expect much interesting thing on
that, I just remove that for now.
==
Hi Leon,
What is the output of ls -lah /mnt/galaxyIndices/alignments/maf/?
Also, you may what to use additional sub-directory structure for your file
locations in case you want to add more alignments later, e.g.,
/mnt/galaxyIndices/hg19/maf/10_way_multiz/ or similiar
Also, note that although
Hi Dan,
Here are the output:
==
hmei@ubuntu:~$ ls -lah /mnt/galaxyIndices/alignments/maf/
total 236G
drwxrwsr-x 2 postgres postgres 4.0K Sep 10 00:08 .
drwxrwsr-x 4 postgres postgres 4.0K Sep 9 16:27 ..
-rw-rw-r-- 1 postgres postgres 13G Oct 31 2009 chr10.maf
-rw-rw-r-- 1 postgres postgres
Hi Leon,
Can you see if there is any info reported reported by running the MAF
consistency checking script at scripts/tools/maf/check_loc_file.py
path/to/maf_index.loc?
You'll need to make sure that required dependencies (e.g. galaxy_root/lib and
galaxy_root/eggs) are included in your
