MicrobeAnnotator: DB build error on step 9

I have tried to create the MicrobeAnnotator with and without Aspera, using the conda installation (v2.0.5) as well as pip installation (v2.0.4) and I keep getting the following errors on step 9 (steps 1-8 worked returned no errors):

With Aspera:

2021-05-03 11:59:58,370 [INFO]: This is MicrobeAnnotator v2.0.5
2021-05-03 11:59:58,371 [INFO]: I will download and format the databases I use.
2021-05-03 11:59:58,371 [INFO]: Creating database folders
2021-05-03 11:59:58,371 [INFO]: Step 9
2021-05-03 11:59:58,371 [INFO]: Downloading protein fasta files using Aspera Connect.
Traceback (most recent call last):
  File "/gpfs1/scratch/ryan/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 445, in <module>
    main()
  File "/gpfs1/scratch/ryan/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 437, in main
    single_step, aspera, keep_temp, bin_path)
  File "/gpfs1/scratch/ryan/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 175, in database_duilder
    refseq_prot = refseq.refseq_fasta_downloader(database_directory)
  File "/gpfs1/scratch/ryan/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/refseq_data_downloader.py", line 61, in refseq_fasta_downloader
    ascp_key = get_aspera_key()
  File "/gpfs1/scratch/ryan/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/refseq_data_downloader.py", line 277, in get_aspera_key
    install_folder = Path(path_to_ascp).parents[1]
  File "/gpfs1/scratch/ryan/miniconda3/envs/microbeannotator/lib/python3.7/pathlib.py", line 1027, in __new__
    self = cls._from_parts(args, init=False)
  File "/gpfs1/scratch/ryan/miniconda3/envs/microbeannotator/lib/python3.7/pathlib.py", line 674, in _from_parts
    drv, root, parts = self._parse_args(args)
  File "/gpfs1/scratch/ryan/miniconda3/envs/microbeannotator/lib/python3.7/pathlib.py", line 658, in _parse_args
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType

Without Aspera (--no_aspera flag):

2021-04-30 16:48:40,896 [INFO]: This is MicrobeAnnotator v2.0.4
2021-04-30 16:48:40,896 [INFO]: I will download and format the databases I use.
2021-04-30 16:48:40,896 [INFO]: Creating database folders
2021-04-30 16:48:40,897 [INFO]: Step 9
2021-04-30 16:48:40,897 [INFO]: Downloading protein fasta files using wget.
2021-04-30 19:36:28,292 [INFO]: Merging protein files
Traceback (most recent call last):
  File "/gpfs1/apps/anaconda/envs/microbeannotator/bin/microbeannotator_db_builder", line 445, in <module>
    main()
  File "/gpfs1/apps/anaconda/envs/microbeannotator/bin/microbeannotator_db_builder", line 437, in main
    single_step, aspera, keep_temp, bin_path)
  File "/gpfs1/apps/anaconda/envs/microbeannotator/bin/microbeannotator_db_builder", line 178, in database_duilder
    database_directory, threads)
  File "/gpfs1/apps/anaconda/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/refseq_data_downloader.py", line 162, in refseq_fasta_downloader_wget
    copyfileobj(temp_file,merged_db)
  File "/gpfs1/apps/anaconda/envs/microbeannotator/lib/python3.7/shutil.py", line 79, in copyfileobj
    buf = fsrc.read(length)
  File "/gpfs1/apps/anaconda/envs/microbeannotator/lib/python3.7/gzip.py", line 300, in read1
    return self._buffer.read1(size)
  File "/gpfs1/apps/anaconda/envs/microbeannotator/lib/python3.7/_compression.py", line 68, in readinto
    data = self.read(len(byte_view))
  File "/gpfs1/apps/anaconda/envs/microbeannotator/lib/python3.7/gzip.py", line 482, in read
    uncompress = self._decompressor.decompress(buf, size)
zlib.error: Error -3 while decompressing data: invalid code lengths set

About this issue

Original URL
State: open
Created 3 years ago
Reactions: 1
Comments: 16 (3 by maintainers)

Most upvoted comments

@angeliqueray

I also faced the same issue! While going trough the code/error message, I figured out that the problem was caused by the line number 61 in microbeannotator/database/refseq_data_downloader.py file. “ascp_key = get_aspera_key()”

So, I changed it to: ascp_key = “/home/[username]/.aspera/connect/etc/asperaweb_id_dsa.openssh” # replace [username] with your username.

Did the same thing for line number 186. For some weird reason, this solved the problem for the aspera option.

Hopefully, this helps!

nihesh7391 on Nov 15, 2021

I had the same issue and solved it by adding aspera to path.

Make sure that Aspera added to your path.

(Usually it will be installed in your home under your user in "/home/[user]/.aspera/connect/bin", it will show you where)

Take note of this installation folder and, for your peace of mind lets add this folder to your PATH:

Add the following line to your ~/.bashrc file: export PATH="$PATH:/home/[user]/.aspera/connect/bin"
Note: Replace [user] by your username

Now reload the ~/.bashrc file with: source ~/.bashrc

Now you have installed Aspera Connect!

seoldh on Oct 14, 2021