I’m running qiime2-2019.7 in a conda environment, and I’m trying to run Qemistree using qiime2 by it’s q2-qemistree plugin. (seems like not many people are using q2-qemistree).
I’m following the q2-qemistree tutorial step by step but I got stuck at generating a hierarchy of molecules (earlier steps are working well and I checked all inputs and outputs).
When trying to run ‘qiime qemistree make-hierarchy’ like below,
qiime qemistree make-hierarchy \ --i-csi-results fingerprints.qza \ --i-feature-tables feature-table.qza \ --o-tree qemistree.qza \ --o-feature-table feature-table-hashed.qza \ --o-feature-data feature-data.qza
I got the error message like below.
Traceback (most recent call last)
File “/home/user/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</home/user/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-217>”, line 2, in make_hierarchy
File “/home/user/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
File “/home/user/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/home/user/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_qemistree/_hierarchy.py”, line 126, in make_hierarchy
File “/home/user/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_qemistree/_process_fingerprint.py”, line 95, in process_csi_results
collated_fps = collate_fingerprint(csi_result, qc_properties, metric)
File “/home/user/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_qemistree/_process_fingerprint.py”, line 28, in collate_fingerprint
fpfoldrs = os.listdir(csi_result)
FileNotFoundError: [Errno 2] No such file or directory: ‘/data/tmp/qiime2-archive-397d8bha/072dce7a-0c53-46ed-b2a4-a01013fe1828/data/csi-output’
I have tried to overwrite the tmp directory by
export TMPDIR =’/data’
(I also checked that the variable is set by running ‘echo $TMPDIR’)
However, it still gives the same type of error
([Errno 2] No such file or directory: ‘/data/qiime2-archive…’)
I browsed TMPDIR directory and keep looking at it while q2-qemistree is running,
and I saw some temporary directories were created but they were gone in few seconds.
Then I checked the directory permissions for TMPDIR but couldn’t fined any issues.
Any help would be greatly appreciated.