Error in Mask Alignment

User Support
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1

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

2

Looks like the input file aligned-rep-seqs.qza must be corrupted somehow. Could you please try running this command and let us know what happens:
qiime tools validate aligned-rep-seqs.qza

Any chance you could also share that file here? (you can send in a PM if you don't want it to be public)

Did you create that file yourself or download from somewhere? You mention SLURM; was that file created on your cluster with an earlier command, or did you transfer that file from elsewhere? In either case, I recommend that you retrieve this file again if possible.

3

iime tools validate aligned-rep-seqs.qza
Traceback (most recent call last):
File "/home/hrigoni/.conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/tools.py", line 379, in validate
artifact = qiime2.sdk.Artifact.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'

There was a problem loading aligned-rep-seqs.qza as a QIIME 2 Artifact:

Bad CRC-32 for file '3a59bd27-3684-4b7c-a426-b339efbe33d8/provenance/artifacts/57b286b1-a838-4d94-a84e-3b72308a81c2/action/action.yaml'

See above for debug info.

I was worried about that. It looks like it is corrupt. I created that file on our cluster. I reran it and validated it again and it appears to work. I'll send you that file anyway.

4

Oh good news. If the new file is working there is no need to send, unless if this issue occurs again. Good luck!