Error -3 while decompressing data: invalid block type

(Cassey) #1

Hi everyone, I am running qiime 2019.1. I got the error below after running demux summarize:

Plugin error from demux:

Error -3 while decompressing data: invalid block type

Debug info has been saved to /tmp/qiime2-q2cli-err-s55ydt1u.log

I used the following command:
qiime demux summarize --i-data DUXXXdemux-paired-end.qza --o-visualization DUXXXdemux.qzv

Any ideas on how to fix this?

Thanks

(Matthew Ryan Dillon) #2

Hi there @ccbriggs! Sorry to hear things aren’t going well, it looks like something is corrupt here. Can you run the following and provide the results here? Thanks!

qiime tools validate DUXXXdemux-paired-end.qza

:t_rex:

(Liyah Smith) #3

Hello, I am runnig QIIME2 version 2019.1 through the Virtual Box and I am also getting the same error message from using the Greengenes 16S database from QIIME2 DataResources to classify my representative sequences using the classify-consensus-blast command:

Command:

qiime feature-classifier classify-consensus-blast \

–i-query ‘/media/sf_QIIME2DATA/LSmith/sequencedata/050218Sillcus515F-full.cluseq.qza’
–i-reference-reads ‘/media/sf_QIIME2DATA/LSmith/sequencedata/gg-13-8-otus.refseq.qza’
–i-reference-taxonomy ‘/media/sf_QIIME2DATA/LSmith/sequencedata/gg-13-8-otus.reftax.qza’
–p-maxaccepts 1
–p-perc-identity 0.99
–p-strand plus
–o-classification ‘/media/sf_QIIME2DATA/LSmith/sequencedata/050218Sillcus515F-full.taxclass.qza’

Error:

Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.1/bin/qiime”, line 11, in
sys.exit(qiime())
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 764, in call
return self.main(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 717, in main
rv = self.invoke(ctx)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 555, in invoke
return callback(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 244, in call
arguments, missing_in, verbose, quiet = self.handle_in_params(kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 326, in handle_in_params
kwargs, fallback=cmd_fallback)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/handlers.py”, line 375, in get_value
artifact = qiime2.sdk.Result.load(path)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 66, in load
archiver = archive.Archiver.load(filepath)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/core/archive/archiver.py”, line 305, in load
rec = archive.mount(path)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/core/archive/archiver.py”, line 204, in mount
root = self.extract(filepath)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/core/archive/archiver.py”, line 215, in extract
zf.extract(name, path=str(filepath))
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/zipfile.py”, line 1507, in extract
return self._extract_member(member, path, pwd)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/zipfile.py”, line 1579, in _extract_member
shutil.copyfileobj(source, target)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/shutil.py”, line 79, in copyfileobj
buf = fsrc.read(length)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/zipfile.py”, line 872, in read
data = self._read1(n)
File “/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/zipfile.py”, line 948, in _read1
data = self._decompressor.decompress(data, n)
zlib.error: Error -3 while decompressing data: invalid block type

I did not get the error until this step. Should my input data be changed or reformatted?

(Matthew Ryan Dillon) #4

Please run qiime tools validate separately on each of your input files, and report the results back here. Thanks!

(Liyah Smith) #5

Hello, here are the results of validating my input files:

qiime tools validate ‘/media/sf_QIIME2DATA/LSmith/sequencedata/050218Sillcus515F-full.repseq.qza’
Result /media/sf_QIIME2DATA/LSmith/sequencedata/050218Sillcus515F-full.repseq.qza appears to be valid at level=max.

qiime tools validate ‘/media/sf_QIIME2DATA/LSmith/sequencedata/silva99.refseq.qza’
Result /media/sf_QIIME2DATA/LSmith/sequencedata/silva99.refseq.qza does not appear to be valid at level=max:

Changed files:
- ‘data/dna-sequences.fasta’: 43757f9f124e54ad5c9a51cbb7b9eb16 -> 8e8669b1c7e71b81dba9da38337c6641

qiime tools validate ‘/media/sf_QIIME2DATA/LSmith/sequencedata/silva99.reftax.qza’
Result /media/sf_QIIME2DATA/LSmith/sequencedata/silva99.reftax.qza does not appear to be valid at level=max:

Changed files:
- ‘data/taxonomy.tsv’: 5249d917c473deee53cd739f945c1994 -> 52d22af4c8781064d3c6c6d97d3dedbf

(Matthew Ryan Dillon) #6

Wow, looks like we have our answer — silva99.refseq.qza and silva99.reftax.qza both appear to be corrupt (the data file signatures are slightly different from what QIIME 2 first saw when the files were created). I think the best course of action here is to start over with those two files - re-import and re-process them up to this point, then try again. Not sure how the problem happened in the first place, but my guess is something on your machine hiccuped and lead to this. :safety_pin: