Hello Ray users,
I am currently running assemblies of simulated data of human chromosome 21 with
Ray to see what sort of 'hybrid' coverage is needed to effectively assemble
primate genomes. With this trial, I use simulated short (250 insert size)
Illumina reads and simulated PacBio reads, attempting to leverage Ray's ability
to use different NGS reads. However, I am getting a persistent error even
before producing contigs--somewhere while estimating outer differences of the
paired reads. I have checked to make sure that the MPI used is the same as Ray
was compiled with, which seems like it was an issue in another archived post,
so this is not the issue. Below is the command and the produced error file.
Any troubleshooting suggestions would be most appreciated!
Thanks,
Ryan
#!/bin/bash
#PBS -l nodes=4:ppn=8
#PBS -l mem=60g
#PBS -l walltime=02:00:00:00
#PBS -q hpc-uni
module unload compiler/gnu/4.5
module load compiler/gnu/4.5
module unload mpi/openmpi/1.4.3-gnu-4.5
module load mpi/openmpi/1.4.3-gnu-4.5
module unload bio/ray/2.3.0
module load bio/ray/2.3.0
mpiexec -n 32 Ray -k 31 -p 40xillumina_1.fastq 40xillumina_2.fastq -s
depth10_001.fastq -o Ray_Hybrid
Error File:
Ray does parallel de novo genome assemblies of next-gen sequencing data.
INFO: Please read module help and references therein for additional infos.
[n030102:23315] *** Process received signal ***
[n030102:23315] Signal: Segmentation fault (11)
[n030102:23315] Signal code: (128)
[n030102:23315] Failing at address: (nil)
[n030102:23315] [ 0] /lib64/libpthread.so.0 [0x2b299ef6ebe0]
[n030102:23315] [ 1] /opt/bwgrid/mpi/openmpi/1.4.3-gnu-4.5/lib/libmpi.so.0
[0x2b299c816c04]
[n030102:23315] [ 2] /opt/bwgrid/mpi/openmpi/1.4.3-gnu-4.5/lib/libmpi.so.0
[0x2b299c8a5c03]
[n030102:23315] [ 3] /opt/bwgrid/mpi/openmpi/1.4.3-gnu-4.5/lib/libmpi.so.0
[0x2b299c89cd30]
[n030102:23315] [ 4]
/opt/bwgrid/mpi/openmpi/1.4.3-gnu-4.5/lib/libmpi.so.0(MPI_Isend+0x173)
[0x2b299c7f5eb3]
[n030102:23315] [ 5]
Ray(_ZN15MessagesHandler12sendMessagesEP12StaticVectorP13RingAllocator+0xbb)
[0x5bcecb]
[n030102:23315] [ 6] Ray(_ZN11ComputeCore12sendMessagesEv+0x156) [0x5c04e6]
[n030102:23315] [ 7] Ray(_ZN11ComputeCore15runWithProfilerEv+0x5d1) [0x5c4491]
[n030102:23315] [ 8] Ray(_ZN11ComputeCore3runEv+0xbc) [0x5c5bdc]
[n030102:23315] [ 9] Ray(_ZN7Machine5startEv+0x1766) [0x47e506]
[n030102:23315] [10] Ray(main+0x28e) [0x47959e]
[n030102:23315] [11] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b299f198994]
[n030102:23315] [12] Ray(_ZNSt8ios_base4InitD1Ev+0x39) [0x479209]
[n030102:23315] *** End of error message ***
--------------------------------------------------------------------------
mpiexec noticed that process rank 22 with PID 23315 on node n030102 exited on
signal 11 (Segmentation fault).
------------------------------------------------------------------------------
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