traitar pfam /tmp/traitar-pfam uses too much RAM

[fungs]

The above command gets killed after exhausting system memory on a desktop 4 GiB machine. The download procedure should not use that much memory.

[fungs]

More information about the relevant code:

Traceback (most recent call last):
  File "/tmp/traitar/bin/traitar", line 309, in <module>
    args.func(args)
  File "/tmp/traitar/local/lib/python2.7/site-packages/traitar/get_external_data.py", line 28, in download
    out_f.write(zf.read())
  File "/usr/lib/python2.7/gzip.py", line 254, in read
    self._read(readsize)
  File "/usr/lib/python2.7/gzip.py", line 313, in _read
    self._add_read_data( uncompress )
  File "/usr/lib/python2.7/gzip.py", line 331, in _add_read_data
    self.extrabuf = self.extrabuf[offset:] + data
MemoryError

[aweimann]

Thanks for your comment. I fixed this and it will be distributed in the next version. Until then you can download and extract Pfam-A.hmm.gz manually as documented in the wiki.