STAR Alignment for E. Coli: Segmentation Error
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5 months ago
gt • 0

I have tried many different things to get this STAR alignment working for RNA-seq (E. coli). In building the reference genome I made sure to include "--genomeSAindexNbases 10" in my gene index code. Where ten is equal to min(14,log_2(4.6 million)/2 - 1) which is 10. This works fine and I am able to build the reference genome. However, when I run my alignment code

[e37n08:78586] *** Process received signal ***
[e37n08:78586] Signal: Segmentation fault (11)
[e37n08:78586] Signal code: Address not mapped (1)
[e37n08:78586] [ 0] [0x2000000504d8]
[e37n08:78586] [ 1] [0x7ffffef335f0]
[e37n08:78586] [ 2] /gpfs/alpine/syb105/proj-shared/Personal/atown/Libraries/Summit/Anaconda3/envs/tensorflow_summit/lib/python3.6/site-packages/mpi4py/MPI.cpython-36m-powerpc64le-linux-gnu.so(+0xe95e4)[0x200000f495e4]
[e37n08:78586] [ 3] /gpfs/alpine/syb105/proj-shared/Personal/atown/Libraries/Summit/Anaconda3/envs/tensorflow_summit/lib/python3.6/site-packages/mpi4py/MPI.cpython-36m-powerpc64le-linux-gnu.so(+0x33cd0)[0x200000e93cd0]
[e37n08:78586] [ 4] python(PyModule_ExecDef+0xd8)[0x1121fb068]
[e37n08:78586] [ 5] python(+0x25b1a8)[0x1121fb1a8]
[e37n08:78586] [ 6] python(PyCFunction_Call+0x1a4)[0x11207a7a4]


I have tried reducing the --genomeSAIndexNbases down to a smaller number but this is not solving the error. Anyone have any idea how to solve this issue? Any help appreciated.

RNA-Seq STAR alignment software error • 147 views