mcall crashes on overlapClip BAM files (bamutils)

[sklages]

HI,

I am using mcall on bsmaped WGBS data which has been overlap-clipped by bamutils overlapClip[1]. mcall crashes on data with a core cump :

strace:

[...]
[pid 29925] read(3, "CC\nGAGCAGGTTGCCCATTGAAGAGGCGGCGG"..., 8191) = 8191
[pid 29925] read(3, "TGCTGTTCTTAGAGACTGAACA\nATTAAAATA"..., 8191) = 8191
[pid 29925] read(3, "gcttaaaaagaaaaaggaaaaagaagacacag"..., 8191) = 8191
[pid 29925] read(3, "atggctgagaa\ngcacctgaaaaaaagtgttc"..., 8191) = 8191
[pid 29925] read(3, "aaggtagaaataacccaagggtcactcaacc\n"..., 8191) = 8191
[pid 29925] read(3, "\ncccacccacccccactcccctacccacccac"..., 8191) = 8191
[pid 29925] read(3, "tctcttagaatctgcatgac\nctctgaccagg"..., 8191) = 8191
[pid 29925] read(3, "ttctgtcgcacaaattatagtctttcatgaag"..., 8191) = 8191
[pid 29925] read(3, "atcttggca\nccctcttctggtgtgcaggcag"..., 8191) = 8191
[pid 29925] read(3, "CTGTAAAACACCCCACAGATAAGTAATGT\nGC"..., 8191) = 8191
[pid 29925] read(3, "ggcgtggcagaacgaatgagcaggaagctcca"..., 8191) = 5411
[pid 29925] read(3, "", 8191)           = 0
[pid 29925] close(3)                    = 0
[pid 29925] mmap(NULL, 8392704, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS|MAP_STACK, -1, 0) = 0x7fce847f1000
[pid 29925] mprotect(0x7fce847f1000, 4096, PROT_NONE) = 0
[pid 29925] clone(strace: Process 29951 attached
child_stack=0x7fce84ff0e70, flags=CLONE_VM|CLONE_FS|CLONE_FILES|CLONE_SIGHAND|CLONE_THREAD|CLONE_SYSVSEM|CLONE_SETTLS|CLONE_PARENT_SETTID|CLONE_CHILD_CLEARTID, parent_tidptr=0x7fce84ff19d0, tls=0x7fce84ff1700, child_tidptr=0x7fce84ff19d0) = 29951
[pid 29951] set_robust_list(0x7fce84ff19e0, 24 <unfinished ...>
[pid 29925] futex(0x7fce94010f34, FUTEX_WAIT_PRIVATE, 1, NULL <unfinished ...>
[pid 29951] <... set_robust_list resumed> ) = 0
[pid 29951] write(1, "Start processing file AM-WGBS-00"..., 72Start processing file MYSAMPLE_3m_test.srt.oc.rdp.bam on chrom chr10
) = 72
[pid 29951] open("MYSAMPLE_3m_test.srt.oc.rdp.bam.chr10_skip.bed", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
[pid 29951] write(3, "#chrom\tstart\tend\tratio\ttotalC\tme"..., 48) = 48
[pid 29951] open("MYSAMPLE_3m_test.srt.oc.rdp.bam", O_RDONLY) = 4
[pid 29951] mprotect(0x7fce8c021000, 8192, PROT_READ|PROT_WRITE) = 0
[pid 29951] lseek(4, -28, SEEK_END)     = 599820951
[pid 29951] read(4, "\37\213\10\4\0\0\0\0\0\377\6\0BC\2\0\33\0\3\0\0\0\0\0\0\0\0\0", 28) = 28
[pid 29951] lseek(4, 0, SEEK_SET)       = 0
[pid 29951] read(4, "\37\213\10\4\0\0\0\0\0\377\6\0BC\2\0N3", 18) = 18
[pid 29951] read(4, "\325}k\214#\311}_\355\354\356\255Nc\301\2526\r\24\201\30`3;'&\213\336c7\337\355"..., 13117) = 13117
[pid 29951] mprotect(0x7fce8c023000, 8192, PROT_READ|PROT_WRITE) = 0
[pid 29951] mprotect(0x7fce8c025000, 4096, PROT_READ|PROT_WRITE) = 0
[pid 29951] mprotect(0x7fce8c026000, 4096, PROT_READ|PROT_WRITE) = 0
[pid 29951] mprotect(0x7fce8c027000, 40960, PROT_READ|PROT_WRITE) = 0
[pid 29951] mprotect(0x7fce8c031000, 40960, PROT_READ|PROT_WRITE) = 0
[pid 29951] futex(0x830090, FUTEX_WAKE_PRIVATE, 2147483647) = 0
[pid 29951] write(2, "terminate called after throwing "..., 48terminate called after throwing an instance of ') = 48
[pid 29951] write(2, "std::out_of_range", 17std::out_of_range) = 17
[pid 29951] write(2, "'\n", 2'
)          = 2
[pid 29951] write(2, "  what():  ", 11  what():  ) = 11
[pid 29951] write(2, "basic_string::substr", 20basic_string::substr) = 20
[pid 29951] write(2, "\n", 1
)           = 1
[pid 29951] rt_sigprocmask(SIG_UNBLOCK, [ABRT], NULL, 8) = 0
[pid 29951] tgkill(29916, 29951, SIGABRT) = 0
[pid 29951] --- SIGABRT {si_signo=SIGABRT, si_code=SI_TKILL, si_pid=29916, si_uid=184} ---
[pid 29916] <... futex resumed>)        = ?
[pid 29925] <... futex resumed>)        = ?
[pid 29925] +++ killed by SIGABRT (core dumped) +++
[pid 29951] +++ killed by SIGABRT (core dumped) +++
+++ killed by SIGABRT (core dumped) +++
Aborted (core dumped)

Any idea where to start looking for the problem?