Question: Gkno: Sort-Multiple-Bam-Error
gravatar for Viktor Ljungström
6.3 years ago by
Viktor Ljungström40 wrote:


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

ADD COMMENTlink modified 6.3 years ago by Chase Miller400 • written 6.3 years ago by Viktor Ljungström40

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 ?

ADD REPLYlink written 6.3 years ago by Chase Miller400

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?

ADD REPLYlink written 6.3 years ago by Viktor Ljungström40
gravatar for Chase Miller
6.3 years ago by
Chase Miller400
University of Utah
Chase Miller400 wrote:

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.

ADD COMMENTlink written 6.3 years ago by Chase Miller400

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.

ADD REPLYlink written 6.3 years ago by Viktor Ljungström40

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

ADD REPLYlink written 6.3 years ago by Chase Miller400

This has been fixed in version 0.44

ADD REPLYlink written 6.2 years ago by Chase Miller400
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