kraken won't build + other stuff

[karoraw1]

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?

[[email protected]@login-node03 ~]$ cd scratch/metaWRAP_DBs/
[[email protected]@login-node03 kraken_db]$ interact -p lrgmem -t 480 -n 24 -m 600G
Tasks:    24
Cores/task: 1
Total cores: 24
Walltime: 480
Reservation:   
Queue:    lrgmem
Command submitted: salloc -J interact -N 1-1 -n 24 -c 1 --mem=600G --time=480 -p lrgmem srun --pty bash
salloc: Granted job allocation 19524778
Using standard path: /cm/shared/apps/gsl/1.16
Using standard path: /cm/shared/apps/gsl/1.16
[email protected] currently using 6G of 20G available in home directory.
Filling home quota will prevent the ability to log in.
[[email protected]@bigmem0041 kraken_db]$ source ~/.bash_profile 
Using standard path: /cm/shared/apps/gsl/1.16
Using standard path: /cm/shared/apps/gsl/1.16
[email protected] currently using 6G of 20G available in home directory.
Filling home quota will prevent the ability to log in.
[[email protected]@bigmem0041 kraken_db]$ source activate metawrap-env
(metawrap-env) [[email protected]@bigmem0041 kraken_db]$ kraken-build --standard --threads 24 --db MY_KRAKEN_DATABASE
Possible unintended interpolation of @jhu in string at /home-3/[email protected]/scratch/miniconda2/envs/metawrap-env/bin/kraken-build line 28.
Global symbol "@jhu" requires explicit package name (did you forget to declare "my @jhu"?) at /home-3/[email protected]/scratch/miniconda2/envs/metawrap-env/bin/kraken-build line 28.
BEGIN not safe after errors--compilation aborted at /home-3/[email protected]/scratch/miniconda2/envs/metawrap-env/bin/kraken-build line 32.

[karoraw1]

strangely, it works fine when you download kraken from https://ccb.jhu.edu/software/kraken/ and run the kraken-build in the scripts directory

[karoraw1]

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.

[ursky]

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/[email protected]/scratch/miniconda2/libexec";
After: my $KRAKEN_DIR = '/home-2/[email protected]/scratch/miniconda2/libexec';

[ursky]

And thank you for letting me know about the CheckM database change! I fixed the metaWRAP database installation page to reflect this change.