pbalign issue: blasr v5.1 seems to be not integrated with pbalign

Question

[Pawel Osipowski]

When installing the newest blasr and pbalign through github tutorials I get this after running pbalign.

ERROR: --sam is no longer supported, use --bam, then translate from .bam to .sam
[ERROR] 2016-09-10 11:00:09,126Z [root Execute 67] BlasrService returned a non-zero exit status. [INFO] 2016-09-10T13:00:09 [blasr] started.
ERROR: --sam is no longer supported, use --bam, then translate from .bam to .sam
[INFO] 2016-09-10 11:00:09,126Z [pbalign.pbalignrunner _pacbio_main_runner 153] exiting with return code 1 in 0.28 sec.

How to overcome this problem or install older blasr? Please, help me

[Pawel Osipowski]

It seems they work on this. Some additional info is here: https://github.com/PacificBiosciences/pbalign/issues/48

Answer 1

[WouterDeCoster]

My interpretation is that the --sam flag is no longer supported as such throwing an error, how did you run the code?

The installation of blasr is the most horrible installation I have encountered, so far.

[Pawel Osipowski]

It's horrible experience to me too :) especially from half a year ago when I was doing it on an old system. I followed those recently: https://github.com/PacificBiosciences/pbalign/blob/master/doc/howto.rst https://github.com/PacificBiosciences/blasr/wiki/Step-by-step-blasr-installation-example

your interpretation is as mine. the problem is pbalign is still working the old way on blasr

Answer 2

[Pawel Osipowski]

It looks like they fixed this issue by producing blasr v5.3. You have to install pbalign and blasr through their new installing platform called pitchfork. From my experience be very careful using clean environment they offer. Right now I'm trying to get back to my system environment after I terminated session with their clean environment. If anyone can help, please see this: http://unix.stackexchange.com/questions/309891/no-access-to-system-binaries-after-switching-off-terminal-with-bash-session-with Thanks