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http://dib-lab.github.io/dammit/
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TaskError - taskid:download:Pfam-A.hmm.gz #144

Open Maya0801 opened 5 years ago

Maya0801 commented 5 years ago

Hello!

I get an error while trying to install databases for dammit, version v1.0rc2.

I am working on my university cluster(Linux 2.6.32-573.26.1.el6.x86_64 x86_64), and I installed dammit with conda using these commands:

export PATH=/data/home/steindler/mbritstei/programs/anaconda2/bin:$PATH

conda create --name dammit python=3.6

source activate dammit

conda install dammit

then when I run dammit databases

I get:

submodule: databases

Database Check

Info

  • Database Directory: /data/home/steindler/mbritstei/.dammit/databases
  • Doit Database: /data/home/steindler/mbritstei/.dammit/databases/databases.doit.db

Some tasks out of date!

Out-of-date tasks:

  • cmpress:Rfam
  • download:BUSCO-metazoa
  • download:OrthoDB
  • download:Pfam-A
  • download:Rfam
  • gunzip:OrthoDB
  • gunzip:Pfam-A
  • gunzip:Rfam
  • hmmpress:Pfam-A
  • lastdb:OrthoDB

Must install databases to continue. To do so, run dammit databases --install. If you have already installed them, make sure you've given the correct location to --database-dir or have exported the $DAMMIT_DB_DIR environment variable.

so I tried bothdammit databases --install and dammit databases --install --database-dir /data/home/steindler/mbritstei/.dammit/databases

for both I get the same error:

Run Tasks

  • [ ] download:Pfam-A.hmm.gz:
    • Cmd: curl -o Pfam-A.hmm.gz ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam28.0/Pfam-A.hmm.gz
    • Python: function check_hash curl: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory TaskError - taskid:download:Pfam-A.hmm.gz PythonAction Error Traceback (most recent call last): File "/data/home/steindler/mbritstei/programs/anaconda2/envs/dammit/lib/python3.6/site-packages/dammit/tasks/shell.py", line 33, in hashfile f = gzip.open(path, "rb") File "/data/home/steindler/mbritstei/programs/anaconda2/envs/dammit/lib/python3.6/gzip.py", line 53, in open binary_file = GzipFile(filename, gz_mode, compresslevel) File "/data/home/steindler/mbritstei/programs/anaconda2/envs/dammit/lib/python3.6/gzip.py", line 163, in init fileobj = self.myfileobj = builtins.open(filename, mode or 'rb') FileNotFoundError: [Errno 2] No such file or directory: 'Pfam-A.hmm.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/data/home/steindler/mbritstei/programs/anaconda2/envs/dammit/lib/python3.6/site-packages/dammit/tasks/shell.py", line 36, in hashfile f = open(path, "rb") FileNotFoundError: [Errno 2] No such file or directory: 'Pfam-A.hmm.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/data/home/steindler/mbritstei/programs/anaconda2/envs/dammit/lib/python3.6/site-packages/doit/action.py", line 424, in execute returned_value = self.py_callable(*self.args, **kwargs) File "/data/home/steindler/mbritstei/programs/anaconda2/envs/dammit/lib/python3.6/site-packages/dammit/tasks/shell.py", line 52, in check_hash if expected == hashfile(target_fn): File "/data/home/steindler/mbritstei/programs/anaconda2/envs/dammit/lib/python3.6/site-packages/dammit/tasks/shell.py", line 39, in hashfile raise RuntimeError('Function hashfile could not find referenced file.'\ RuntimeError: Function hashfile could not find referenced file. Is there a problem with curl?

######################################## TaskError - taskid:download:Pfam-A.hmm.gz download:Pfam-A.hmm.gz :

  • Checking hash of Pfam-A.hmm.gz

download:Pfam-A.hmm.gz :

thanks for the help!

Maya