Gkno: Sort-Multiple-Bam-Error

Question

[Viktor Ljungström]

Hi,

I'm trying to set up gkno but have come across some errors on the way when trying the run-test pipeline.

1. First time it stopped at the build-reference task and then reported the error "/bin/sh: /"pathonmycomputer"/gkno/gkno_launcher/tools/MOSAIK/bin/MosaikBuild: No such file or directory" I looked into named folder and realized that it was empty. To resolve this i placed the bin files from the latest Mosaikbuild into this directory which seemed to solve the problem. Is this a possible bug that anyone else has seen?

2. When retrying after replacing the files everything runs smoothly until the sort-multiple-bam-step. Gkno then reports "Error 1" and in the error log i find "bamtools sort ERROR: could not open /"pathonmycomputer"/gkno/gknolauncher/simulatedreads1.multiple.bam for reading... Aborting." There is no file called simulatedreads_1.multiple.bam in the project folder either. I'm a bit stuck here, has anyone else seen this error?

I'm test running this on Mac OSX 10.8.2 and it's gkno version 0.42. My java version is 1.6.0_37 so that shouldn't be a problem.

Best, Viktor

[Chase Miller]

Hi Viktor, I'm part of the gkno team. From the first error you hit with MosaikBuild missing from the <..>/bin directory, it sounds like there may have been a problem with the build step. Did you see any errors when you first ran ./gkno build ?

[Viktor Ljungström]

Hi Chase, thanks for your reply. Yes i suspected something in the build process and tried reinstalling several times (in different directories etc) but never got any error messages and no error logs were found in the /logs-directory. I just tried installing it on my home computer with the exact same result (same system settings as above so i don't know what i expected...)

Are there any earlier releases available to try out?

Answer 1

[Chase Miller]

We've just noticed some instances where an environment flag on MacOSX isn't being set correctly. Try typing one of the following (depending whether you're 32/64bit) from the command-line

export BLD_PLATFORM=macosx

export BLD_PLATFORM=macosx64

Then download a fresh copy of gkno and build it. This should fix the problem.

[Viktor Ljungström]

Epic, works like a charm!

Big thanks for your help and for sharing this platform. Now I just have to convince the clusterguys that this is the future, shouldn't be a problem.

[Chase Miller]

No problem! We'll make sure to get this fix into the github repo.

[Chase Miller]

This has been fixed in version 0.44 gkno.me