Hi, I keep getting an error in the mask alignment step.
qiime alignment mask \
--i-alignment aligned-rep-seqs.qza
--o-masked-alignment masked-aligned-rep-seqs.qza
Traceback (most recent call last):
File "/home/hrigoni/.conda/envs/qiime2-2018.8/bin/qiime", line 11, in
sys.exit(qiime())
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 244, in call
arguments, missing_in, verbose, quiet = self.handle_in_params(kwargs)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 326, in handle_in_params
kwargs, fallback=cmd_fallback)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/handlers.py", line 375, in get_value
artifact = qiime2.sdk.Result.load(path)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/result.py", line 65, in load
archiver = archive.Archiver.load(filepath)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 299, in load
rec = archive.mount(path)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 199, in mount
root = self.extract(filepath)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 210, in extract
zf.extract(name, path=str(filepath))
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/zipfile.py", line 1335, in extract
return self._extract_member(member, path, pwd)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/zipfile.py", line 1399, in _extract_member
shutil.copyfileobj(source, target)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/shutil.py", line 79, in copyfileobj
buf = fsrc.read(length)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/zipfile.py", line 844, in read
data = self._read1(n)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/zipfile.py", line 934, in _read1
self._update_crc(data)
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/zipfile.py", line 862, in _update_crc
raise BadZipFile("Bad CRC-32 for file %r" % self.name)
zipfile.BadZipFile: Bad CRC-32 for file '3a59bd27-3684-4b7c-a426-b339efbe33d8/provenance/artifacts/57b286b1-a838-4d94-a84e-3b72308a81c2/action/action.yaml'
I have tried it both using a SLURM script for a batch job and through the control. I have Qiime on both a virtual box, and set up in a conda environment. I get the same error in both.
I am running the following:
System versions
Python version: 3.5.5
QIIME 2 release: 2018.8
QIIME 2 version: 2018.8.0
q2cli version: 2018.8.0
Installed plugins
alignment: 2018.8.0
composition: 2018.8.0
cutadapt: 2018.8.0
dada2: 2018.8.0
deblur: 2018.8.0
demux: 2018.8.0
diversity: 2018.8.0
emperor: 2018.8.0
feature-classifier: 2018.8.0
feature-table: 2018.8.0
gneiss: 2018.8.0
longitudinal: 2018.8.0
metadata: 2018.8.0
phylogeny: 2018.8.0
quality-control: 2018.8.0
quality-filter: 2018.8.0
sample-classifier: 2018.8.0
taxa: 2018.8.0
types: 2018.8.0
vsearch: 2018.8.0