-
Notifications
You must be signed in to change notification settings - Fork 45
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Error while running the iMetAOS test_pipeline_test.sh #249
Comments
The pipeline is just calling which so if it is in the path they should be found. For MetaGeneMark it is looking for gmhmmp, for Reapr it is looking for reapr, and for FRC it is looking for FRCbam. You can also add a symlink from the Utilities/cpp/Linux-amd64 folder to the tools. It would be FRCBam to your FRC install folder, REAPR to your reapr install folder, and gmhmmp binary for MetaGeneMark. I think it should be using
|
Thanks for your reply Sergey, Here is the ls -l for the REAPR directory inside /metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/ Also, inside the src dir: [root@tcmc_sandbox2 REAPR]# ls -l src |
REAPR cannot be found because your install looks incomplete or is a different version (metAMOS uses 1.0.16). The installation should add a symlink named reapr pointing to reapr.pl:
This is what metAMOS is looking for and not finding. |
Aah.. I have a different version – I have 1.0.18 Not sure how to uninstall it and install a clean copy of 1.0.16 Any suggestions ? Thanks so much for your help. From: Sergey Koren [mailto:notifications@github.com] _CAUTION:_ This email is not from a BCM Source. Only click links or open attachments you know are safe. REAPR cannot be found because your install looks incomplete or is a different version (metAMOS uses 1.0.16). The installation should add a symlink named reapr pointing to reapr.pl: $ tail -n 20 install.sh " cd $rootdir/src make cd .. ln -s src/reapr.pl reapr echo " Reapr compiled All done! Run ./reapr for usage. Read the manual manual.pdf for full instructions " This is what metAMOS is looking for and not finding. — |
You can try symlinking src/reapr.pl as reapr or just renaming reapr.pl to reapr since it is already a symlink in your folder. |
IT WORKED!! Now it find reapr ! Ok now we need to tackle the next issue. Ive just opened another ticket #250 Not sure why it suddenly stops at the FINDORFs stage.. didn't do that before. I've removed the -a soap flag from the run_pipline_test.sh and re-running it now. Same error :( Sabeen -------- Original message -------- _CAUTION:_ This email is not from a BCM Source. Only click links or open attachments you know are safe. You can try symlinking src/reapr.pl as reapr or just renaming reapr.pl to reapr since it is already a symlink in your folder. You are receiving this because you authored the thread. |
Hi,
I've installed MetAMOS and iMetAMOS on my linux box and tried to run the test pipleine (run_pipeline_test.sh) and got the following warnings and errors:
A few questions:
I HAVE definitely installed MetaGeneMark, REAPR and FRC_Align I've included the executable (and bin directories) in PATH but the test scrip still cannot find them.
I'm not sure why the test stopped abruptly at POSTPROCESSING.
How can I re-run the test pipeline cleanly ?
here is what the POSTPROCESS.log file shows in the /Test/test/ directory:
The text was updated successfully, but these errors were encountered: