I have done a full PS run using only the DNGNGWU markers (+concat) and all seems to run. However, no trees are produced.
In the run_info.txt, all steps are run. See below:
Chunk 1 sequences processed 20b5b0b6d73b20a830ab3bbeb042afc6
Chunk 1 Search completed 2017-10-24 12:34:08 2017-10-24 15:33:01 10733
Chunk 1 Align completed 2017-10-24 15:33:01 2017-10-24 15:33:14 13
Chunk 1 Place completed 2017-10-24 15:33:14 2017-10-24 15:33:14 0
Chunk 1 Summarize completed 2017-10-24 15:33:14 2017-10-24 15:33:23 9
Chunk 2 sequences processed dcaf5f7c95921f7bd0e232b92c4e0d84
Chunk 2 Search completed 2017-10-24 15:33:23 2017-10-24 17:51:58 8315
Chunk 2 Align completed 2017-10-24 17:51:58 2017-10-24 17:52:12 14
Chunk 2 Place completed 2017-10-24 17:52:12 2017-10-24 17:52:12 0
Chunk 2 Summarize completed 2017-10-24 17:52:12 2017-10-24 17:52:21 9
Chunk 3 sequences processed 3c01814394c7a0a765557b75cee1b6e1
Chunk 3 Search completed 2017-10-24 17:52:21 2017-10-24 20:18:39 8778
Chunk 3 Align completed 2017-10-24 20:18:39 2017-10-24 20:18:53 14
Chunk 3 Place completed 2017-10-24 20:18:53 2017-10-24 20:18:53 0
Chunk 3 Summarize completed 2017-10-24 20:18:53 2017-10-24 20:19:02 9
Chunk 4 sequences processed a7161aa1be467bee6d37f542052ee8d0
Chunk 4 Search completed 2017-10-24 20:19:02 2017-10-24 20:52:13 1991
Chunk 4 Align completed 2017-10-24 20:52:13 2017-10-24 20:52:21 8
Chunk 4 Place completed 2017-10-24 20:52:21 2017-10-24 20:52:21 0
Chunk 4 Summarize completed 2017-10-24 20:52:21 2017-10-24 20:52:27 6
So then in the blast_dir the marker_summary.txt is full of hits totaling to 13495.
Then in the align directory, there are several alignment files, 1, 2, 3, 4 for each of the above chunks run.
Then in the tree.dir there is nothing.
In addition, all of the standalone summary files are empty.
It appears that all goes except for the pplace step placing all of these aligned files into the tree. Any thoughts on why manipulating the database would hinder this step from going forwards?
Mike