r-make

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FAQ.

1. Q: I received an error "EXITING because of FATAL ERROR: waited too long for the other job to finish loading the genomeSuccess".
A: Sometimes STAR fails to load the genome. The best thing to do is type 'ipcs'. The output will look something like this:

------ Shared Memory Segments --------
key shmid owner perms bytes nattch status
0x17001700 3375122 paz2005 666 28271287966 0

Remove the failed attempt at loading the genome using ipcrm. For example, 'ipcrm -m 3375122'. Then, before starting r-make again, attempt to load the genome manually; for example, to load hg19: /path/to/rmake-1.0/third-party/star --genomeDir /path/to/rmake-1.0/references/indexes/hg19/ --genomeLoad LoadAndExit . If successful, try running r-make again.

2. Q: I received an error "error while loading shared libraries: libbamtools.so.2.2.3".
A: Make sure bamtools is installed. If so, remember to export the bamtools library path. To export the libary path, type:
export LD_LIBRARY_PATH=/PATH/TO/BAMTOOLS/lib:$LD_LIBRARY_PATH .
To make this change permanent, add it to your ~/.bashrc .

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p. zumbo