catchsegv sambamba markdup --hash-table-size=500000 --remove-duplicates -t 19 --overflow-list-size=1000000 --sort-buffer-size=4096 --tmpdir=. bam_in.bam bam_out.bam sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018 LDC 1.13.0 / DMD v2.083.1 / LLVM7.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6) finding positions of the duplicate reads in the file... sorted 419305 end pairs and 376 single ends (among them 0 unmatched pairs) collecting indices of duplicate reads... done in 78 ms found 396697 duplicates collected list of positions in 0 min 0 sec removing duplicates... Segmentation fault (core dumped) *** Segmentation fault Register dump: RAX: 00005559bf87e710 RBX: 00007f4e034373c0 RCX: 0000000000000028 RDX: 00005559bfa43000 RSI: 00007f4e034373c0 RDI: 2727272626262626 RBP: 00007f4e03436000 R8 : 0000000000000000 R9 : 00007f4dc5911000 R10: 00007f4f203d9938 R11: 0000000000000286 R12: ffffffffffffff70 R13: 00000000000138e2 R14: 00005559bfa5df10 R15: 00007f4e03436010 RSP: 00007ffe27e91860 RIP: 00007f4f1f833804 EFLAGS: 00010202 CS: 0033 FS: 0000 GS: 0000 Trap: 0000000d Error: 00000000 OldMask: 00000000 CR2: 00000000 FPUCW: 0000037f FPUSW: 00000020 TAG: 00005559 RIP: bf907ffe RDP: 27e9160c ST(0) 0000 0000000000000000 ST(1) 0000 0000000000000000 ST(2) 0000 0000000000000000 ST(3) 0000 0000000000000000 ST(4) 0000 0000000000000000 ST(5) 0000 0000000000000000 ST(6) ffff 8000000000000000 ST(7) c950 c950cdcc16e5f6c8 mxcsr: 1fa0 XMM0: 0000000000000000000000007fff7f20 XMM1: 0000000000000000000000007fff7f20 XMM2: 0000000000000000000000007fff7f20 XMM3: 0000000000000000000000007fff7f20 XMM4: 0000000000000000000000007fff7f20 XMM5: 0000000000000000000000007fff7f20 XMM6: 0000000000000000000000007fff7f20 XMM7: 0000000000000000000000007fff7f20 XMM8: 0000000000000000000000007fff7f20 XMM9: 0000000000000000000000007fff7f20 XMM10: 0000000000000000000000007fff7f20 XMM11: 0000000000000000000000007fff7f20 XMM12: 0000000000000000000000007fff7f20 XMM13: 0000000000000000000000007fff7f20 XMM14: 0000000000000000000000007fff7f20 XMM15: 0000000000000000000000007fff7f20 Backtrace: [SNIP_ENV_PATH]/bin/../lib/libphobos2-ldc-shared.so.83(_D3std11parallelism8TaskPool16tryDeleteExecuteMFPSQBwQBv12AbstractTaskZv+0x4)[0x7f4f1f833804] sambamba(+0x151d1e)[0x5559bf87ed1e] [SNIP_ENV_PATH]/bin/../lib/libdruntime-ldc-shared.so.83(rt_finalizeFromGC+0xab)[0x7f4f203892db] [SNIP_ENV_PATH]/bin/../lib/libdruntime-ldc-shared.so.83(_D2gc4impl12conservativeQw3Gcx5sweepMFNbZm+0xfe)[0x7f4f20373e0e] [SNIP_ENV_PATH]/bin/../lib/libdruntime-ldc-shared.so.83(_D2gc4impl12conservativeQw3Gcx11fullcollectMFNbbZm+0x1a3)[0x7f4f20370f83] [SNIP_ENV_PATH]/bin/../lib/libdruntime-ldc-shared.so.83(_D2gc4impl12conservativeQw3Gcx8bigAllocMFNbmKmkxC8TypeInfoZPv+0xd7)[0x7f4f20372c17] [SNIP_ENV_PATH]/bin/../lib/libdruntime-ldc-shared.so.83(_D2gc4impl12conservativeQw14ConservativeGC__T9runLockedS_DQCeQCeQCcQCnQBs12mallocNoSyncMFNbmkKmxC8TypeInfoZPvS_DQEgQEgQEeQEp10mallocTimelS_DQFiQFiQFgQFr10numMallocslTmTkTmTxQCzZQFcMFNbKmKkKmKxQDsZQDl+0x94)[0x7f4f2036f234] [SNIP_ENV_PATH]/bin/../lib/libdruntime-ldc-shared.so.83(_DThn16_2gc4impl12conservativeQw14ConservativeGC6qallocMFNbmkxC8TypeInfoZS4core6memory8BlkInfo_+0x53)[0x7f4f203718c3] [SNIP_ENV_PATH]/bin/../lib/libdruntime-ldc-shared.so.83(gc_qalloc+0x20)[0x7f4f203762f0] [SNIP_ENV_PATH]/bin/../lib/libdruntime-ldc-shared.so.83(_D4core6memory2GC6qallocFNaNbmkxC8TypeInfoZSQBqQBo8BlkInfo_+0x12)[0x7f4f20363872] [SNIP_ENV_PATH]/bin/../lib/libdruntime-ldc-shared.so.83(_d_newarrayU+0x16f)[0x7f4f203883ff] sambamba(+0x151e48)[0x5559bf87ee48] sambamba(+0x16bd35)[0x5559bf898d35] sambamba(+0x17c950)[0x5559bf8a9950] sambamba(+0x104b14)[0x5559bf831b14] sambamba(+0x112881)[0x5559bf83f881] sambamba(+0x11178d)[0x5559bf83e78d] [SNIP_ENV_PATH]/bin/../lib/libdruntime-ldc-shared.so.83(_D2rt6dmain211_d_run_mainUiPPaPUAAaZiZ6runAllMFZv+0x50)[0x7f4f20385110] [SNIP_ENV_PATH]/bin/../lib/libdruntime-ldc-shared.so.83(_d_run_main+0x1f6)[0x7f4f20384f26] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f4f1eda9b97] sambamba(+0xa093f)[0x5559bf7cd93f] Memory map: 5559bf72d000-5559bfa3b000 r-xp 00000000 08:21 34357074 [SNIP_ENV_PATH]/bin/sambamba 5559bfa3b000-5559bfa4d000 r--p 0030d000 08:21 34357074 [SNIP_ENV_PATH]/bin/sambamba 5559bfa4d000-5559bfa68000 rw-p 0031f000 08:21 34357074 [SNIP_ENV_PATH]/bin/sambamba 5559bffea000-5559c01be000 rw-p 00000000 00:00 0 [heap] 7f4dc5911000-7f4ec8000000 rw-p 00000000 00:00 0 7f4ec8000000-7f4ec8021000 rw-p 00000000 00:00 0 7f4ec8021000-7f4ecc000000 ---p 00000000 00:00 0 7f4eccaff000-7f4ed0000000 rw-p 00000000 00:00 0 7f4ed0000000-7f4ed0043000 rw-p 00000000 00:00 0 7f4ed0043000-7f4ed4000000 ---p 00000000 00:00 0 7f4ed4000000-7f4ed404b000 rw-p 00000000 00:00 0 7f4ed404b000-7f4ed8000000 ---p 00000000 00:00 0 7f4ed8000000-7f4ed8021000 rw-p 00000000 00:00 0 7f4ed8021000-7f4edc000000 ---p 00000000 00:00 0 7f4edc000000-7f4edc043000 rw-p 00000000 00:00 0 7f4edc043000-7f4ee0000000 ---p 00000000 00:00 0 7f4ee0000000-7f4ee0021000 rw-p 00000000 00:00 0 7f4ee0021000-7f4ee4000000 ---p 00000000 00:00 0 7f4ee4000000-7f4ee4021000 rw-p 00000000 00:00 0 7f4ee4021000-7f4ee8000000 ---p 00000000 00:00 0 7f4ee8000000-7f4ee8043000 rw-p 00000000 00:00 0 7f4ee8043000-7f4eec000000 ---p 00000000 00:00 0 7f4eec000000-7f4eec021000 rw-p 00000000 00:00 0 7f4eec021000-7f4ef0000000 ---p 00000000 00:00 0 7f4ef0000000-7f4ef0021000 rw-p 00000000 00:00 0 7f4ef0021000-7f4ef4000000 ---p 00000000 00:00 0 7f4ef45fa000-7f4ef4ffa000 rw-p 00000000 00:00 0 7f4ef4ffa000-7f4ef4ffb000 ---p 00000000 00:00 0 7f4ef4ffb000-7f4ef57fb000 rw-p 00000000 00:00 0 7f4ef57fb000-7f4ef57fc000 ---p 00000000 00:00 0 7f4ef57fc000-7f4ef5ffc000 rw-p 00000000 00:00 0 7f4ef5ffc000-7f4ef5ffd000 ---p 00000000 00:00 0 7f4ef5ffd000-7f4ef67fd000 rw-p 00000000 00:00 0 7f4ef67fd000-7f4ef67fe000 ---p 00000000 00:00 0 7f4ef67fe000-7f4ef6ffe000 rw-p 00000000 00:00 0 7f4ef6ffe000-7f4ef6fff000 ---p 00000000 00:00 0 7f4ef6fff000-7f4ef77ff000 rw-p 00000000 00:00 0 7f4ef77ff000-7f4ef7800000 ---p 00000000 00:00 0 7f4ef7800000-7f4ef8000000 rw-p 00000000 00:00 0 7f4ef8000000-7f4ef8021000 rw-p 00000000 00:00 0 7f4ef8021000-7f4efc000000 ---p 00000000 00:00 0 7f4efc000000-7f4efc043000 rw-p 00000000 00:00 0 7f4efc043000-7f4f00000000 ---p 00000000 00:00 0 7f4f00000000-7f4f00043000 rw-p 00000000 00:00 0 7f4f00043000-7f4f04000000 ---p 00000000 00:00 0 7f4f04000000-7f4f04043000 rw-p 00000000 00:00 0 7f4f04043000-7f4f08000000 ---p 00000000 00:00 0 7f4f08000000-7f4f08043000 rw-p 00000000 00:00 0 7f4f08043000-7f4f0c000000 ---p 00000000 00:00 0 7f4f0c000000-7f4f0c043000 rw-p 00000000 00:00 0 7f4f0c043000-7f4f10000000 ---p 00000000 00:00 0 7f4f10000000-7f4f10043000 rw-p 00000000 00:00 0 7f4f10043000-7f4f14000000 ---p 00000000 00:00 0 7f4f14036000-7f4f140b8000 rw-p 00000000 00:00 0 7f4f140f9000-7f4f147f9000 rw-p 00000000 00:00 0 7f4f147f9000-7f4f147fa000 ---p 00000000 00:00 0 7f4f147fa000-7f4f14ffa000 rw-p 00000000 00:00 0 7f4f14ffa000-7f4f14ffb000 ---p 00000000 00:00 0 7f4f14ffb000-7f4f157fb000 rw-p 00000000 00:00 0 7f4f157fb000-7f4f157fc000 ---p 00000000 00:00 0 7f4f157fc000-7f4f15ffc000 rw-p 00000000 00:00 0 7f4f15ffc000-7f4f15ffd000 ---p 00000000 00:00 0 7f4f15ffd000-7f4f167fd000 rw-p 00000000 00:00 0 7f4f167fd000-7f4f167fe000 ---p 00000000 00:00 0 7f4f167fe000-7f4f16ffe000 rw-p 00000000 00:00 0 7f4f16ffe000-7f4f16fff000 ---p 00000000 00:00 0 7f4f16fff000-7f4f177ff000 rw-p 00000000 00:00 0 7f4f177ff000-7f4f17800000 ---p 00000000 00:00 0 7f4f17800000-7f4f18000000 rw-p 00000000 00:00 0 7f4f18000000-7f4f18043000 rw-p 00000000 00:00 0 7f4f18043000-7f4f1c000000 ---p 00000000 00:00 0 7f4f1c083000-7f4f1c084000 ---p 00000000 00:00 0 7f4f1c084000-7f4f1c884000 rw-p 00000000 00:00 0 7f4f1c884000-7f4f1c885000 ---p 00000000 00:00 0 7f4f1c885000-7f4f1d085000 rw-p 00000000 00:00 0 7f4f1d085000-7f4f1d086000 ---p 00000000 00:00 0 7f4f1d086000-7f4f1d886000 rw-p 00000000 00:00 0 7f4f1d886000-7f4f1d887000 ---p 00000000 00:00 0 7f4f1d887000-7f4f1e087000 rw-p 00000000 00:00 0 7f4f1e087000-7f4f1e088000 ---p 00000000 00:00 0 7f4f1e088000-7f4f1ed88000 rw-p 00000000 00:00 0 7f4f1ed88000-7f4f1ef6f000 r-xp 00000000 08:01 2078 /lib/x86_64-linux-gnu/libc-2.27.so 7f4f1ef6f000-7f4f1f16f000 ---p 001e7000 08:01 2078 /lib/x86_64-linux-gnu/libc-2.27.so 7f4f1f16f000-7f4f1f173000 r--p 001e7000 08:01 2078 /lib/x86_64-linux-gnu/libc-2.27.so 7f4f1f173000-7f4f1f175000 rw-p 001eb000 08:01 2078 /lib/x86_64-linux-gnu/libc-2.27.so 7f4f1f175000-7f4f1f179000 rw-p 00000000 00:00 0 7f4f1f179000-7f4f1f17c000 r-xp 00000000 08:01 2081 /lib/x86_64-linux-gnu/libdl-2.27.so 7f4f1f17c000-7f4f1f37b000 ---p 00003000 08:01 2081 /lib/x86_64-linux-gnu/libdl-2.27.so 7f4f1f37b000-7f4f1f37c000 r--p 00002000 08:01 2081 /lib/x86_64-linux-gnu/libdl-2.27.so 7f4f1f37c000-7f4f1f37d000 rw-p 00003000 08:01 2081 /lib/x86_64-linux-gnu/libdl-2.27.so 7f4f1f37d000-7f4f1f384000 r-xp 00000000 08:01 2181 /lib/x86_64-linux-gnu/librt-2.27.so 7f4f1f384000-7f4f1f583000 ---p 00007000 08:01 2181 /lib/x86_64-linux-gnu/librt-2.27.so 7f4f1f583000-7f4f1f584000 r--p 00006000 08:01 2181 /lib/x86_64-linux-gnu/librt-2.27.so 7f4f1f584000-7f4f1f585000 rw-p 00007000 08:01 2181 /lib/x86_64-linux-gnu/librt-2.27.so 7f4f1f585000-7f4f1f75b000 r--p 00000000 08:21 36965399 [SNIP_ENV_PATH]/lib/libphobos2-ldc-shared.so.2.0.83 7f4f1f75b000-7f4f1f8dd000 r-xp 001d6000 08:21 36965399 [SNIP_ENV_PATH]/lib/libphobos2-ldc-shared.so.2.0.83 7f4f1f8dd000-7f4f1f9a5000 r--p 00358000 08:21 36965399 [SNIP_ENV_PATH]/lib/libphobos2-ldc-shared.so.2.0.83 7f4f1f9a5000-7f4f1f9b9000 r--p 0041f000 08:21 36965399 [SNIP_ENV_PATH]/lib/libphobos2-ldc-shared.so.2.0.83 7f4f1f9b9000-7f4f1f9fa000 rw-p 00433000 08:21 36965399 [SNIP_ENV_PATH]/lib/libphobos2-ldc-shared.so.2.0.83 7f4f1f9fa000-7f4f1f9fb000 rw-p 00000000 00:00 0 7f4f1f9fb000-7f4f1fb98000 r-xp 00000000 08:01 2082 /lib/x86_64-linux-gnu/libm-2.27.so 7f4f1fb98000-7f4f1fd97000 ---p 0019d000 08:01 2082 /lib/x86_64-linux-gnu/libm-2.27.so 7f4f1fd97000-7f4f1fd98000 r--p 0019c000 08:01 2082 /lib/x86_64-linux-gnu/libm-2.27.so 7f4f1fd98000-7f4f1fd99000 rw-p 0019d000 08:01 2082 /lib/x86_64-linux-gnu/libm-2.27.so 7f4f1fd99000-7f4f1fdb3000 r-xp 00000000 08:01 2179 /lib/x86_64-linux-gnu/libpthread-2.27.so 7f4f1fdb3000-7f4f1ffb2000 ---p 0001a000 08:01 2179 /lib/x86_64-linux-gnu/libpthread-2.27.so 7f4f1ffb2000-7f4f1ffb3000 r--p 00019000 08:01 2179 /lib/x86_64-linux-gnu/libpthread-2.27.so 7f4f1ffb3000-7f4f1ffb4000 rw-p 0001a000 08:01 2179 /lib/x86_64-linux-gnu/libpthread-2.27.so 7f4f1ffb4000-7f4f1ffb8000 rw-p 00000000 00:00 0 7f4f1ffb8000-7f4f1ffbc000 r-xp 00000000 08:01 2076 /lib/x86_64-linux-gnu/libSegFault.so 7f4f1ffbc000-7f4f201bb000 ---p 00004000 08:01 2076 /lib/x86_64-linux-gnu/libSegFault.so 7f4f201bb000-7f4f201bc000 r--p 00003000 08:01 2076 /lib/x86_64-linux-gnu/libSegFault.so 7f4f201bc000-7f4f201bd000 rw-p 00004000 08:01 2076 /lib/x86_64-linux-gnu/libSegFault.so 7f4f201bd000-7f4f201e4000 r-xp 00000000 08:01 2074 /lib/x86_64-linux-gnu/ld-2.27.so 7f4f20248000-7f4f202ba000 rw-p 00000000 00:00 0 7f4f202ba000-7f4f202bd000 r--p 00000000 08:21 34343364 [SNIP_ENV_PATH]/lib/libgcc_s.so.1 7f4f202bd000-7f4f202ca000 r-xp 00003000 08:21 34343364 [SNIP_ENV_PATH]/lib/libgcc_s.so.1 7f4f202ca000-7f4f202cd000 r--p 00010000 08:21 34343364 [SNIP_ENV_PATH]/lib/libgcc_s.so.1 7f4f202cd000-7f4f202ce000 r--p 00012000 08:21 34343364 [SNIP_ENV_PATH]/lib/libgcc_s.so.1 7f4f202ce000-7f4f202cf000 rw-p 00013000 08:21 34343364 [SNIP_ENV_PATH]/lib/libgcc_s.so.1 7f4f202cf000-7f4f202d1000 rw-p 00000000 00:00 0 7f4f202d1000-7f4f2034c000 r--p 00000000 08:21 36965395 [SNIP_ENV_PATH]/lib/libdruntime-ldc-shared.so.2.0.83 7f4f2034c000-7f4f2039f000 r-xp 0007b000 08:21 36965395 [SNIP_ENV_PATH]/lib/libdruntime-ldc-shared.so.2.0.83 7f4f2039f000-7f4f203c6000 r--p 000ce000 08:21 36965395 [SNIP_ENV_PATH]/lib/libdruntime-ldc-shared.so.2.0.83 7f4f203c6000-7f4f203c7000 ---p 000f5000 08:21 36965395 [SNIP_ENV_PATH]/lib/libdruntime-ldc-shared.so.2.0.83 7f4f203c7000-7f4f203cf000 r--p 000f5000 08:21 36965395 [SNIP_ENV_PATH]/lib/libdruntime-ldc-shared.so.2.0.83 7f4f203cf000-7f4f203d9000 rw-p 000fd000 08:21 36965395 [SNIP_ENV_PATH]/lib/libdruntime-ldc-shared.so.2.0.83 7f4f203d9000-7f4f203da000 rw-p 00000000 00:00 0 7f4f203e2000-7f4f203e4000 rw-p 00000000 00:00 0 7f4f203e4000-7f4f203e5000 r--p 00027000 08:01 2074 /lib/x86_64-linux-gnu/ld-2.27.so 7f4f203e5000-7f4f203e6000 rw-p 00028000 08:01 2074 /lib/x86_64-linux-gnu/ld-2.27.so 7f4f203e6000-7f4f203e7000 rw-p 00000000 00:00 0 7ffe27e74000-7ffe27e95000 rw-p 00000000 00:00 0 [stack] 7ffe27ecc000-7ffe27ecf000 r--p 00000000 00:00 0 [vvar] 7ffe27ecf000-7ffe27ed1000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]