Appending Taxonomy Error about amptk

[nextgenusfs]

I believe this has been fixed in newer versions, please upgrade to the latest and let me know if problem persists.

[MycoMap]

Will do

[bsmoda]

I also got an error with the taxonomy step, the biom wasn't created:
[02/22/19 17:05:25]: biom convert -i ../cluster/its2_mosaic_all.final.txt -o ../cluster/its2_mosaic_all.biom.tmp --table-type OTU table --to-json
[02/22/19 17:05:26]: Traceback (most recent call last):
File "/mnt/data2/lbcb/conda/envs/amptk/bin/biom", line 6, in
from biom.cli import cli
File "/mnt/data2/lbcb/conda/envs/amptk/lib/python2.7/site-packages/biom/init.py", line 51, in
from .table import Table
File "/mnt/data2/lbcb/conda/envs/amptk/lib/python2.7/site-packages/biom/table.py", line 200, in
from ._filter import _filter
File "init.pxd", line 861, in init biom._filter (biom/_filter.c:6729)
ValueError: numpy.ufunc has the wrong size, try recompiling. Expected 192, got 216

[02/22/19 17:05:26]: biom add-metadata -i ../cluster/its2_mosaic_all.biom.tmp -o ../cluster/its2_mosaic_all.biom --observation-metadata-fp ../cluster/
[02/22/19 17:05:27]: Traceback (most recent call last):
File "/mnt/data2/lbcb/conda/envs/amptk/bin/biom", line 6, in
from biom.cli import cli
File "/mnt/data2/lbcb/conda/envs/amptk/lib/python2.7/site-packages/biom/init.py", line 51, in
from .table import Table
File "/mnt/data2/lbcb/conda/envs/amptk/lib/python2.7/site-packages/biom/table.py", line 200, in
from ._filter import _filter
File "init.pxd", line 861, in init biom._filter (biom/_filter.c:6729)
ValueError: numpy.ufunc has the wrong size, try recompiling. Expected 192, got 216

The complete log file is attached below.
its2_mosaic_all.amptk-taxonomy.log

[nextgenusfs]

Looks like this is not an amptk error -- but rather an error from your install of the biom tool. Try to run this manually and you'll see the error. You need to fix your biom install -- likely a numpy/biom compiliation issue.

biom convert -i ../cluster/its2_mosaic_all.final.txt -o ../cluster/its2_mosaic_all.biom.tmp --table-type OTU table --to-json

Here is your error in the logfile:

[02/22/19 17:05:25]: biom convert -i ../cluster/its2_mosaic_all.final.txt -o ../cluster/its2_mosaic_all.biom.tmp --table-type OTU table --to-json
[02/22/19 17:05:26]: Traceback (most recent call last):
  File "/mnt/data2/lbcb/conda/envs/amptk/bin/biom", line 6, in <module>
    from biom.cli import cli
  File "/mnt/data2/lbcb/conda/envs/amptk/lib/python2.7/site-packages/biom/__init__.py", line 51, in <module>
    from .table import Table
  File "/mnt/data2/lbcb/conda/envs/amptk/lib/python2.7/site-packages/biom/table.py", line 200, in <module>
    from ._filter import _filter
  File "__init__.pxd", line 861, in init biom._filter (biom/_filter.c:6729)
ValueError: numpy.ufunc has the wrong size, try recompiling. Expected 192, got 216

[02/22/19 17:05:26]: biom add-metadata -i ../cluster/its2_mosaic_all.biom.tmp -o ../cluster/its2_mosaic_all.biom --observation-metadata-fp ../cluster/its2_mosaic_all.qiime.taxonomy.txt -m ../preprocessing/its2_mosaic_all.mapping_file.txt --sc-separated taxonomy --output-as-json
[02/22/19 17:05:27]: Traceback (most recent call last):
  File "/mnt/data2/lbcb/conda/envs/amptk/bin/biom", line 6, in <module>
    from biom.cli import cli
  File "/mnt/data2/lbcb/conda/envs/amptk/lib/python2.7/site-packages/biom/__init__.py", line 51, in <module>
    from .table import Table
  File "/mnt/data2/lbcb/conda/envs/amptk/lib/python2.7/site-packages/biom/table.py", line 200, in <module>
    from ._filter import _filter
  File "__init__.pxd", line 861, in init biom._filter (biom/_filter.c:6729)
ValueError: numpy.ufunc has the wrong size, try recompiling. Expected 192, got 216

Next time please open a new issue unless it is the exact same problem.