"Uncompressing db failed" superfocus_downloadDB.py blast

[bashirhamidi]

Getting the below error due to superfocus_downlaodDB.py not finding the downloaded db.

(super-focus) [x@y ~]$ superfocus_downloadDB.py blast Downloading DB --2018-07-13 14:40:58-- http://edwards.sdsu.edu/superfocus/downloads/db.zip Resolving edwards.sdsu.edu... 130.191.93.70 Connecting to edwards.sdsu.edu|130.191.93.70|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 3527705740 (3.3G) [application/zip] Saving to: "db.zip"

100%[=======================================================================================>] 3,527,705,740 39.3M/s in 49m 22s

2018-07-13 15:30:20 (1.14 MB/s) - "db.zip" saved [3527705740/3527705740]

Uncompressing DB unzip: cannot find or open db/db.zip, db/db.zip.zip or db/db.zip.ZIP. mv: accessing db/': Not a directory rm: cannot removedb/db.zip': Not a directory

Joining files Traceback (most recent call last): File "/home/bah29/packages/anaconda3/envs/super-focus/bin/superfocus_downloadDB.py", line 119, in main() File "/home/bah29/packages/anaconda3/envs/super-focus/bin/superfocus_downloadDB.py", line 108, in main donwloadDBnFormat(aligners) File "/home/bah29/packages/anaconda3/envs/super-focus/bin/superfocus_downloadDB.py", line 46, in donwloadDBnFormat for cluster in os.listdir("db/clusters/") OSError: [Errno 20] Not a directory: 'db/clusters/'

The db is still accessible in the downloaded directly. I have unzipped db as such: (super-focus) [x@y ~]$ unzip "db" -d db2/ Do I need to move the unzipped db to a particular directory?

[metageni]

we have been working to move the tool into bioconda, and it looks like the download script is not working correctly when installing the tool with conda.

quick solution: cd /home/bah29/packages/anaconda3/envs/super-focus/bin/ (which i believe is where conda put the super-focus scripts) and then superfocus_downloadDB.py blast

I will work on the fix in the mean time - sorry about that.