[BUG] tarfile.ReadError: not a gzip file

[Bill-Branson]

Short description of the problem

While installing anvio V8 with "pip install" on a conda environment as per the instructions it fails to gunzip the gz file.

anvi'o version

pip install anvio-8.tar.gz

anvi-self-test --version  ( This fails since it never installs).

System info

CENTOS 7, through conda.

Detailed description of the issue

pip install anvio-8.tar.gz

Processing ./anvio-8.tar.gz
ERROR: Exception:
Traceback (most recent call last):
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/tarfile.py", line 1877, in gzopen
t = cls.taropen(name, mode, fileobj, **kwargs)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/tarfile.py", line 1854, in taropen
return cls(name, mode, fileobj, **kwargs)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/tarfile.py", line 1714, in init
self.firstmember = self.next()
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/tarfile.py", line 2629, in next
raise e
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/tarfile.py", line 2602, in next
tarinfo = self.tarinfo.fromtarfile(self)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/tarfile.py", line 1292, in fromtarfile
buf = tarfile.fileobj.read(BLOCKSIZE)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/gzip.py", line 301, in read
return self._buffer.read(size)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/gzip.py", line 488, in read
if not self._read_gzip_header():
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/gzip.py", line 436, in _read_gzip_header
raise BadGzipFile('Not a gzipped file (%r)' % magic)
gzip.BadGzipFile: Not a gzipped file (b'No')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
status = run_func(*args)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper
return func(self, options, args)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/commands/install.py", line 377, in run
requirement_set = resolver.resolve(
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve
collected = self.factory.collect_root_requirements(root_reqs)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 534, in collect_root_requirements
reqs = list(
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 490, in _make_requirements_from_install_req
cand = self._make_base_candidate_from_link(
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link
self._link_candidate_cache[link] = LinkCandidate(
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in init
super().init(
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in init
self.dist = self._prepare()
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare
dist = self._prepare_distribution()
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution
return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement
return self._prepare_linked_requirement(req, parallel_builds)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/operations/prepare.py", line 596, in _prepare_linked_requirement
local_file = unpack_url(
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/operations/prepare.py", line 178, in unpack_url
unpack_file(file.path, location, file.content_type)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/utils/unpacking.py", line 246, in unpack_file
untar_file(filename, location)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/site-packages/pip/_internal/utils/unpacking.py", line 173, in untar_file
tar = tarfile.open(filename, mode, encoding="utf-8")
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/tarfile.py", line 1824, in open
return func(name, filemode, fileobj, **kwargs)
File "/hpc/apps/miniconda3/4.9.2/envs/anvio-8.0.0/lib/python3.10/tarfile.py", line 1881, in gzopen
raise ReadError("not a gzip file") from e
tarfile.ReadError: not a gzip file

NOTE: I will try and unzip this file and then untar it and then re-tar and re gzip it and see if that might fix it.

########## END ###############

[Bill-Branson]

It might be a corrupted gz file. I will try a few things and see if I can fix it.

Bill

[Bill-Branson]

Problem solved, downloaded the gz file directly to another box. gunziped it. re-gzipped it and moved it to the install platform. NOw it installs with pip install. Please check the one you have at the download site, CURL, was how I grabbed it the failing time and the second time I got it through download on the download page, assets,

https://github.com/merenlab/anvio/releases

top download of the three. There are two source code files and the anvio-8.tar.gz file. Please check them all for validity.

Thanks

Bill

[Bill-Branson]

(anvio-8.0.0) [root@ln01 anvio-8.0.0]# anvi-self-test --version
Anvi'o .......................................: marie (v8)
Python .......................................: 3.10.13

Profile database .............................: 38
Contigs database .............................: 21
Pan database .................................: 16
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2

(anvio-8.0.0) [root@ln01 anvio-8.0.0]#

SUCCESS!!!!!!!!!!!!!!!!!!!!!!!