I have successfully installed qiime2-2018.6 on the linux server and also qiime2-2018.2 on my laptop using docker.
I was trying to run some commands which failed on server but were running on my laptop,Please suggest!
I ran this command on server which ends up in error, whereas the same command works properly on my laptop.
(qiime2-2018.2) root§3209d9fe45ee:/data£ qiime tools import --type EMPPairedEndSequences --input-path emp-paired-end-sequences --output-path emp-paired-end-sequences.qza
No error.
Error on linux server is below:
[pramod@herman-login2 Qiime]$ qiime tools import --type EMPPairedEndSequences --input-path emp-paired-end-sequences --output-path emp-paired-end-sequences.qza
-bash: qiime: command not found
[pramod@herman-login2 Qiime]$ qiime
-bash: qiime: command not found
[pramod@herman-login2 Qiime]$ pwd
/mnt/BioAdHoc/overflow/Groups/KLey/Qiime
[pramod@herman-login2 Qiime]$ source activate qiime2-2018.6
(qiime2-2018.6) [pramod@herman-login2 Qiime]$ qiime tools import --type EMPPairedEndSequences --input-path emp-paired-end-sequences --output-path emp-paired-end-sequences.qza
Traceback (most recent call last):
File "/home/pramod/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/tools.py", line 116, in import_data
view_type=source_format)
File "/home/pramod/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/result.py", line 219, in import_data
return cls._from_view(type_, view, view_type, provenance_capture)
File "/home/pramod/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/result.py", line 250, in _from_view
provenance_capture=provenance_capture)
File "/home/pramod/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 310, in from_data
Format.write(rec, type, format, data_initializer, provenance_capture)
File "/home/pramod/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/core/archive/format/v1.py", line 26, in write
prov_dir, [root / cls.METADATA_FILE, archive_record.version_fp])
File "/home/pramod/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/core/archive/provenance.py", line 315, in finalize
self.path.rename(final_path)
File "/home/pramod/miniconda3/envs/qiime2-2018.6/lib/python3.5/pathlib.py", line 1277, in rename
self._accessor.rename(self, target)
File "/home/pramod/miniconda3/envs/qiime2-2018.6/lib/python3.5/pathlib.py", line 377, in wrapped
return strfunc(str(pathobjA), str(pathobjB), *args)
FileExistsError: [Errno 17] File exists: '/scratch/qiime2-provenance-4o84xp5y' -> '/scratch/qiime2-archive-dgz17z59/f6712e98-38c9-40c0-9b62-1f56b1524052/provenance'
An unexpected error has occurred:
[Errno 17] File exists: '/scratch/qiime2-provenance-4o84xp5y' -> '/scratch/qiime2-archive-dgz17z59/f6712e98-38c9-40c0-9b62-1f56b1524052/provenance'
See above for debug info