Open karoraw1 opened 6 years ago
strangely, it works fine when you download kraken from https://ccb.jhu.edu/software/kraken/ and run the kraken-build
in the scripts
directory
I figured out that the error only happens when the install_kraken.sh
script is provided a path that has an "@" in it. To get around it, I used the kraken-build
script without installing. I also had to manually make
the contents of src
and make that folder visible to $PATH
.
The checkM database is still incorrect though, so this should probs be reopened lol.
Yes, I ran into the Kraken installation issue. If you go to the my $KRAKEN_DIR =
line at the beginning of any of the kraken scripts, you will find they used double quotation marks instead of single to define this path, which causes the error because the script now interprets the '@' in your path as an operator. This is only an issue for some servers because most do not have a '@' symbol in the home directory path. All you have to do to fix this is change the double quotes to single quotes!
For example, in my miniconda2/bin/kraken-build
script, this is what I fixed:
Before: my $KRAKEN_DIR = "/home-2/guritsk1@jhu.edu/scratch/miniconda2/libexec";
After: my $KRAKEN_DIR = '/home-2/guritsk1@jhu.edu/scratch/miniconda2/libexec';
And thank you for letting me know about the CheckM database change! I fixed the metaWRAP database installation page to reflect this change.
one issue i noted was that the link to the checkM database changed and the autoupdate function doesn't work anymore (probs for that reason)
also, kraken won't build on MARCC for whatever reason. I submitted the issue to them as well. did you get around this issue?