links to database not available

[housw]

Hi,

I got the following errors while trying to install MetaCompass, I guess the links have been removed? Could you please update it?

Thanks a lot, Shengwei

./install.sh 
#Installing MetaCompass
g++ -Wall -W -O2 -o ./bin/extractSeq ./src/utils/extractSeq.cpp
g++ -Wall -W -O2 -o ./bin/formatFASTA ./src/utils/formatFASTA.cpp
g++ -Wall -W -O2 -o ./bin/buildcontig ./src/buildcontig/buildcontig.cpp ./src/buildcontig/cmdoptions.cpp ./src/buildcontig/memory.cpp ./src/buildcontig/procmaps.cpp ./src/buildcontig/outputfiles.cpp
wget --no-check-certificate https://gembox.cbcb.umd.edu/metacompass/markers.tar.gz -P ./src
--2018-10-13 01:41:48--  https://gembox.cbcb.umd.edu/metacompass/markers.tar.gz
Resolving gembox.cbcb.umd.edu (gembox.cbcb.umd.edu)... 128.8.120.25
Connecting to gembox.cbcb.umd.edu (gembox.cbcb.umd.edu)|128.8.120.25|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2018-10-13 01:41:49 ERROR 404: Not Found.

cd ./src/metaphyler/
tar -xzvf ./markers.tar.gz
tar (child): ./markers.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
cd ../../
wget --no-check-certificate https://gembox.cbcb.umd.edu/metacompass/refseq.tar.gz
--2018-10-13 01:41:49--  https://gembox.cbcb.umd.edu/metacompass/refseq.tar.gz
Resolving gembox.cbcb.umd.edu (gembox.cbcb.umd.edu)... 128.8.120.25
Connecting to gembox.cbcb.umd.edu (gembox.cbcb.umd.edu)|128.8.120.25|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2018-10-13 01:41:49 ERROR 404: Not Found.

tar -xzvf refseq.tar.gz
tar (child): refseq.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
rm: cannot remove 'refseq.tar.gz': No such file or directory

[ctseto]

Can confirm that this is still the case

[vcepeda]

The repository where I put the references was shutdown last October and haven't reuploaded the database to a new one yet. However, I'm currently working on an improved MetaCompass version to be released in a couple of weeks.

[ctseto]

Thanks for letting us know! Would it be feasible in future to include scripts to reconstruct the markers and refseq files locally? It'll let us update our files in line with RefSeq updates and such, up to the point where NCBI changes their file layout again.

[treangen]

hi @ctseto , the links to database files have been updated; apologies for the delay!

[vcepeda]

I reuploaded the databases we used in the Biorxiv paper (2017). The other one was from a previous version of MetaCompass.