Hi Bastien,
Does the development version of Mira require a newer version of glibc than
the stable branch, by any chance? I keep getting a malloc error when
loading solexa fastq reads during a mapping assembly. Backbone loads
fine....
It goes like this,
Tmp directory is not on a NFS mount, good.
Localtime: Mon Jun 8 10:10:05 2015
Loading reads or assembled contigs as reference backbone from
map_annotatedreference_out.maf type maf
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%] contained 272 contigs. Only the contigs will be
added as backbone.
Loading reads from S2-AP02_S2_L001_R1_001.fastq type fastq
mira: malloc.c:4480: _int_malloc: Assertion `(fwd->size & 0x4) == 0' failed.
Failure, wrapped MIRA process aborted.
The strace output does not seem very helpful,
[000000000098d260] --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_DUMPED,
si_pid=16126, si_status=SIGABRT, si_utime=6910, si_stime=1802} ---
[00000000009cb5f4] fstat(1, {st_dev=makedev(0, 11), st_ino=4,
st_mode=S_IFCHR|0620, st_nlink=1, st_uid=0, st_gid=5, st_blksize=1024,
st_blocks=0, st_rdev=makedev(136, 1), st_atime=2015/06/08-10:47:30,
st_mtime=2015/06/08-10:48:45, st_ctime=2015/06/08-10:21:23}) = 0 <0.000007>
[00000000009cea1a] mmap(NULL, 4096, PROT_READ|PROT_WRITE,
MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x2ac38a66b000 <0.000010>
[0000000000982780] write(1, "Failure, wrapped MIRA process ab"..., 39) = 39
<0.000012>
[00000000009c15f8] exit_group(100) = ?
[????????????????] +++ exited with 100 +++
The only thing I can imagine is that our cluster uses a relatively old
version of glibc (2.12), so there may be a library compatibility issue.
I've attached the full log_assembly, manifest, and strace.out.
Attachment:
manifest.conf
Description: Binary data
Attachment:
strace.out
Description: Binary data
Attachment:
log_assembly
Description: Binary data
