search

bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics
GNU Affero General Public License v3.0
19 stars 9 forks source link

No valid binary found for sga #38

Closed ycl6 closed 6 years ago

ycl6 commented 6 years ago

MATAM spill out these messages complaining not finding the sga binary.

INFO - Graph compaction & Components identification terminated in 63.3342 seconds wall time
INFO - Compressed graph: 472 components

INFO - === LCA labelling ===
INFO - LCA labelling terminated in 7.3417 seconds wall time

INFO - === Contigs assembly ===
INFO - Save components to fastq files
INFO - Assemble components
No valid binary found for sga
No valid binary found for sga
No valid binary found for sga
No valid binary found for sga
No valid binary found for sga
...

I export $MATAM_HOME/sga/src/bin to $PATH but that doesn't help.

ppericard commented 6 years ago

Hi @ycl6, how did you get MATAM ? Through conda or did you compile it yourself ? If you compiled it from the source code, can you send us the trace from the ./build.py script ?

In any case, if you have difficulties running MATAM from the source code, we really encourage you to get it through conda, which makes way easier dealing with dependencies and you wont need to compile it.

ycl6 commented 6 years ago

Hi @ppericard I install MATMA via github source. I found the solution. the sga binary MATAM is looking for is not located in $MATAM_HOME/sga/src/bin but is actually in $MATAM_HOME/sga/src/SGA. Therefore I add that to $PATH too and MATAM is able to complete the job. Thanks.

ppericard commented 6 years ago

@loic-couderc , can you check this is not a bug ?

loic-couderc commented 6 years ago

Hi @ycl6, with the version v1.3.0 of MATAM, if the ./build.py script terminated with no errors which means you have this message at the end of the trace:

2017-09-18 10:09:07,300 - INFO - -- MATAM building complete --
2017-09-18 10:09:07,300 - DEBUG - Building completed in 377.46 seconds
2017-09-18 10:09:07,300 - DEBUG - MATAM building went well. Program executables can be found in MATAM bin directory: ...

Then MATAM should find the SGA binary into $MATAM_HOME/sga/src/SGA without any modification of the PATH. Can you send us the the trace from the ./build.py script?

ycl6 commented 6 years ago

Hi @loic-couderc

I reset $PATH to its original state and reinstall matam but can't reproduce the error anymore. Don't know what happen during my initial build, but all is fine now

2017-09-19 21:03:18,105 - INFO - -- MATAM building complete --
2017-09-19 21:03:18,105 - DEBUG - Building completed in 520.30 seconds
2017-09-19 21:03:18,105 - INFO - MATAM building went well. Program executables can be found in MATAM bin directory: /home/ycl6/tools/matam/bin

Namespace(target='build')
loic-couderc commented 6 years ago

As we cannot reproduce the bug, I close this issue.