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Some tasks out of date!
Out-of-date tasks: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
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?
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:
then when I run
dammit databases
I get:
so I tried both
dammit databases --install
anddammit databases --install --database-dir /data/home/steindler/mbritstei/.dammit/databases
for both I get the same error:
thanks for the help!
Maya