sambamba markdup deadlock in Ubuntu 14.04

[dulunar]

sambamba version: 0.7.1, downloaded binary from release's page and uncompress for using.

LSB Version:    core-2.0-amd64:core-2.0-noarch:core-3.0-amd64:core-3.0-noarch:core-3.1-amd64:core-3.1-noarch:core-3.2-amd64:core-3.2-noarch:core-4.0-amd64:core-4.0-noarch:core-4.1-amd64:core-4.1-noarch:security-4.0-amd64:security-4.0-noarch:security-4.1-amd64:security-4.1-noarch
Distributor ID: Ubuntu
Description:    Ubuntu 14.04.6 LTS
Release:        14.04
Codename:       trusty

Feb 10 01:39, when I used command as follow:

$ /home/luna/Desktop/Software/sambamba/build/sambamba markdup -t 16 -l 9 --tmpdir ./ --sort-buffer-size 4096 ./Bulk.mem.sort.bam ./Bulk.mem.sort.mkdup.bam

But it was deadlock at Feb 10 01:40. There are just 42 bam files：

$ ls ~/work/TempChimera/Bulk/sambatmp/sambamba-pid70545-markdup-oerh
PairedEndsInforbsv0  sorted.13.bam.idx  sorted.18.bam.idx  sorted.22.bam.idx  sorted.27.bam.idx  sorted.31.bam.idx  sorted.36.bam.idx  sorted.40.bam.idx  sorted.6.bam.idx
sorted.0.bam         sorted.14.bam      sorted.19.bam      sorted.23.bam      sorted.28.bam      sorted.32.bam      sorted.37.bam      sorted.41.bam      sorted.7.bam
sorted.0.bam.idx     sorted.14.bam.idx  sorted.19.bam.idx  sorted.23.bam.idx  sorted.28.bam.idx  sorted.32.bam.idx  sorted.37.bam.idx  sorted.41.bam.idx  sorted.7.bam.idx
sorted.10.bam        sorted.15.bam      sorted.1.bam       sorted.24.bam      sorted.29.bam      sorted.33.bam      sorted.38.bam      sorted.42.bam      sorted.8.bam
sorted.10.bam.idx    sorted.15.bam.idx  sorted.1.bam.idx   sorted.24.bam.idx  sorted.29.bam.idx  sorted.33.bam.idx  sorted.38.bam.idx  sorted.42.bam.idx  sorted.8.bam.idx
sorted.11.bam        sorted.16.bam      sorted.20.bam      sorted.25.bam      sorted.2.bam       sorted.34.bam      sorted.39.bam      sorted.4.bam       sorted.9.bam
sorted.11.bam.idx    sorted.16.bam.idx  sorted.20.bam.idx  sorted.25.bam.idx  sorted.2.bam.idx   sorted.34.bam.idx  sorted.39.bam.idx  sorted.4.bam.idx   sorted.9.bam.idx
sorted.12.bam        sorted.17.bam      sorted.21.bam      sorted.26.bam      sorted.30.bam      sorted.35.bam      sorted.3.bam       sorted.5.bam
sorted.12.bam.idx    sorted.17.bam.idx  sorted.21.bam.idx  sorted.26.bam.idx  sorted.30.bam.idx  sorted.35.bam.idx  sorted.3.bam.idx   sorted.5.bam.idx
sorted.13.bam        sorted.18.bam      sorted.22.bam      sorted.27.bam      sorted.31.bam      sorted.36.bam      sorted.40.bam      sorted.6.bam

And I checked the /var/log/messages, I found this:

Feb 10 01:46:09 bioinfo vmunix: [2800262.044005] ------------[ cut here ]------------
Feb 10 01:46:09 bioinfo vmunix: [2800262.044027] WARNING: CPU: 13 PID: 70577 at /build/linux-lts-xenial-lRzcrX/linux-lts-xenial-4.4.0/arch/x86/include/asm/thread_info.h:226
sigsuspend+0x6d/0x70()
Feb 10 01:46:09 bioinfo vmunix: [2800262.044031] Modules linked in: nfsv3 xt_multiport ipmi_devintf ip6t_REJECT nf_reject_ipv6 nf_log_ipv6 xt_hl ip6t_rt nf_conntrack_ipv6 nf
_defrag_ipv6 ipt_REJECT nf_reject_ipv4 nf_log_ipv4 nf_log_common xt_LOG xt_limit xt_tcpudp xt_addrtype nf_conntrack_ipv4 nf_defrag_ipv4 xt_conntrack ip6table_filter ip6_tabl
es nf_conntrack_netbios_ns nf_conntrack_broadcast nf_nat_ftp nf_nat nf_conntrack_ftp nf_conntrack iptable_filter ip_tables x_tables intel_rapl x86_pkg_temp_thermal intel_pow
erclamp coretemp kvm_intel kvm irqbypass crct10dif_pclmul crc32_pclmul ghash_clmulni_intel aesni_intel aes_x86_64 ipmi_ssif lrw gf128mul glue_helper ablk_helper cryptd joyde
v input_leds ast ttm drm_kms_helper sb_edac drm edac_core fb_sys_fops syscopyarea sysfillrect sysimgblt mei_me mei lpc_ich shpchp wmi ipmi_si 8250_fintek rfcomm ipmi_msghand
ler bnep bluetooth parport_pc ppdev acpi_pad mac_hid knem(OE) lp parport nfsd auth_rpcgss nfs_acl binfmt_misc nfs lockd grace sunrpc fscache rdma_ucm(OE) ib_ucm(OE) rdma_cm(
OE) iw_cm(
Feb 10 01:46:09 bioinfo vmunix: onfigfs ib_ipoib(OE) ib_cm(OE) ib_umad(OE) mlx5_fpga_tools(OE) mlx5_ib(OE) mlx5_core(OE) mlxfw(OE) mlx4_ib(OE) ib_uverbs(OE) ib_core(OE) mlx4
_en(OE) vxlan ip6_udp_tunnel udp_tunnel raid10 raid456 async_raid6_recov async_memcpy async_pq async_xor async_tx xor hid_generic mlx4_core(OE) igb mlx_compat(OE) usbhid mpt
3sas i2c_algo_bit ahci dca raid_class hid libahci ptp scsi_transport_sas raid6_pq pps_core libcrc32c raid1 raid0 multipath linear fjes
Feb 10 01:46:09 bioinfo vmunix: [2800262.044237] CPU: 13 PID: 70577 Comm: sambamba Tainted: G        W  OE   4.4.0-148-generic #174~14.04.1-Ubuntu
Feb 10 01:46:09 bioinfo vmunix: [2800262.044242] Hardware name: Sugon I840-G20/80B32-U4/H, BIOS 2.57 05/15/2018
Feb 10 01:46:09 bioinfo vmunix: [2800262.044246]  0000000000000000 ffff881625847ed0 ffffffff813eee37 0000000000000000
Feb 10 01:46:09 bioinfo vmunix: [2800262.044255]  ffffffff81cc5118 ffff881625847f08 ffffffff810829f6 ffff882038e82a00
Feb 10 01:46:09 bioinfo vmunix: [2800262.044263]  00007fc2c57f8c50 00007fc32c6f12b8 00007fc2c57f85a8 0000000000000001
Feb 10 01:46:09 bioinfo vmunix: [2800262.044270] Call Trace:
Feb 10 01:46:09 bioinfo vmunix: [2800262.044288]  [<ffffffff813eee37>] dump_stack+0x63/0x8c
Feb 10 01:46:09 bioinfo vmunix: [2800262.044297]  [<ffffffff810829f6>] warn_slowpath_common+0x86/0xc0
Feb 10 01:46:09 bioinfo vmunix: [2800262.044303]  [<ffffffff81082aea>] warn_slowpath_null+0x1a/0x20
Feb 10 01:46:09 bioinfo vmunix: [2800262.044310]  [<ffffffff81092aed>] sigsuspend+0x6d/0x70
Feb 10 01:46:09 bioinfo vmunix: [2800262.044318]  [<ffffffff81094140>] SyS_rt_sigsuspend+0x40/0x50
Feb 10 01:46:09 bioinfo vmunix: [2800262.044332]  [<ffffffff8182d61b>] entry_SYSCALL_64_fastpath+0x22/0xcb
Feb 10 01:46:09 bioinfo vmunix: [2800262.044337] ---[ end trace 042f2041827a6556 ]---

I tried to use version 0.8.0, still deadlocked. The log:

Feb 10 19:17:10 bioinfo vmunix: [2863321.656228] WARNING: CPU: 67 PID: 16791 at /build/linux-lts-xenial-lRzcrX/linux-lts-xenial-4.4.0/arch/x86/include/asm/thread_info.h:226
sigsuspend+0x6d/0x70()
Feb 10 19:17:10 bioinfo vmunix: [2863321.656231] Modules linked in: nfsv3 xt_multiport ipmi_devintf ip6t_REJECT nf_reject_ipv6 nf_log_ipv6 xt_hl ip6t_rt nf_conntrack_ipv6 nf
_defrag_ipv6 ipt_REJECT nf_reject_ipv4 nf_log_ipv4 nf_log_common xt_LOG xt_limit xt_tcpudp xt_addrtype nf_conntrack_ipv4 nf_defrag_ipv4 xt_conntrack ip6table_filter ip6_tabl
es nf_conntrack_netbios_ns nf_conntrack_broadcast nf_nat_ftp nf_nat nf_conntrack_ftp nf_conntrack iptable_filter ip_tables x_tables intel_rapl x86_pkg_temp_thermal intel_pow
erclamp coretemp kvm_intel kvm irqbypass crct10dif_pclmul crc32_pclmul ghash_clmulni_intel aesni_intel aes_x86_64 ipmi_ssif lrw gf128mul glue_helper ablk_helper cryptd joyde
v input_leds ast ttm drm_kms_helper sb_edac drm edac_core fb_sys_fops syscopyarea sysfillrect sysimgblt mei_me mei lpc_ich shpchp wmi ipmi_si 8250_fintek rfcomm ipmi_msghand
ler bnep bluetooth parport_pc ppdev acpi_pad mac_hid knem(OE) lp parport nfsd auth_rpcgss nfs_acl binfmt_misc nfs lockd grace sunrpc fscache rdma_ucm(OE) ib_ucm(OE) rdma_cm(
OE) iw_cm(
Feb 10 19:17:10 bioinfo vmunix: onfigfs ib_ipoib(OE) ib_cm(OE) ib_umad(OE) mlx5_fpga_tools(OE) mlx5_ib(OE) mlx5_core(OE) mlxfw(OE) mlx4_ib(OE) ib_uverbs(OE) ib_core(OE) mlx4
_en(OE) vxlan ip6_udp_tunnel udp_tunnel raid10 raid456 async_raid6_recov async_memcpy async_pq async_xor async_tx xor hid_generic mlx4_core(OE) igb mlx_compat(OE) usbhid mpt
3sas i2c_algo_bit ahci dca raid_class hid libahci ptp scsi_transport_sas raid6_pq pps_core libcrc32c raid1 raid0 multipath linear fjes
Feb 10 19:17:10 bioinfo vmunix: [2863321.656402] CPU: 67 PID: 16791 Comm: sambamba Tainted: G        W  OE   4.4.0-148-generic #174~14.04.1-Ubuntu
Feb 10 19:17:10 bioinfo vmunix: [2863321.656405] Hardware name: Sugon I840-G20/80B32-U4/H, BIOS 2.57 05/15/2018
Feb 10 19:17:10 bioinfo vmunix: [2863321.656408]  0000000000000000 ffff88185a7f3ed0 ffffffff813eee37 0000000000000000
Feb 10 19:17:10 bioinfo vmunix: [2863321.656413]  ffffffff81cc5118 ffff88185a7f3f08 ffffffff810829f6 ffff8840380ee200
Feb 10 19:17:10 bioinfo vmunix: [2863321.656417]  000000000001a05b 00007f521f066018 00007f51c8ff75e8 00007f521f066144
Feb 10 19:17:10 bioinfo vmunix: [2863321.656422] Call Trace:
Feb 10 19:17:10 bioinfo vmunix: [2863321.656436]  [<ffffffff813eee37>] dump_stack+0x63/0x8c
Feb 10 19:17:10 bioinfo vmunix: [2863321.656443]  [<ffffffff810829f6>] warn_slowpath_common+0x86/0xc0
Feb 10 19:17:10 bioinfo vmunix: [2863321.656446]  [<ffffffff81082aea>] warn_slowpath_null+0x1a/0x20
Feb 10 19:17:10 bioinfo vmunix: [2863321.656450]  [<ffffffff81092aed>] sigsuspend+0x6d/0x70
Feb 10 19:17:10 bioinfo vmunix: [2863321.656455]  [<ffffffff81094140>] SyS_rt_sigsuspend+0x40/0x50
Feb 10 19:17:10 bioinfo vmunix: [2863321.656466]  [<ffffffff8182d61b>] entry_SYSCALL_64_fastpath+0x22/0xcb
Feb 10 19:17:10 bioinfo vmunix: [2863321.656469] ---[ end trace 042f2041827a655d ]---

Now I am trying to use version 0.6.6 for testing if it's work. But it still deadlocked, and there are 298 bam files:

$ ls /home/luna/work/TempChimera/Bulk/sam/sambamba-pid17263-markdup-xxmk
PairedEndsInfocdty0      sorted.130.bam      sorted.165.bam      sorted.19.bam       sorted.233.bam      sorted.268.bam      sorted.32.bam      sorted.67.bam
PairedEndsInfocdty1      sorted.130.bam.idx  sorted.165.bam.idx  sorted.19.bam.idx   sorted.233.bam.idx  sorted.268.bam.idx  sorted.32.bam.idx  sorted.67.bam.idx
PairedEndsInfocdty2      sorted.131.bam      sorted.166.bam      sorted.1.bam        sorted.234.bam      sorted.269.bam      sorted.33.bam      sorted.68.bam
PairedEndsInfocdty3      sorted.131.bam.idx  sorted.166.bam.idx  sorted.1.bam.idx    sorted.234.bam.idx  sorted.269.bam.idx  sorted.33.bam.idx  sorted.68.bam.idx
PairedEndsInfocdty4      sorted.132.bam      sorted.167.bam      sorted.200.bam      sorted.235.bam      sorted.26.bam       sorted.34.bam      sorted.69.bam
PairedEndsInfocdty5      sorted.132.bam.idx  sorted.167.bam.idx  sorted.200.bam.idx  sorted.235.bam.idx  sorted.26.bam.idx   sorted.34.bam.idx  sorted.69.bam.idx
PairedEndsInfocdty6      sorted.133.bam      sorted.168.bam      sorted.201.bam      sorted.236.bam      sorted.270.bam      sorted.35.bam      sorted.6.bam
SingleEndBasicInfofozu0  sorted.133.bam.idx  sorted.168.bam.idx  sorted.201.bam.idx  sorted.236.bam.idx  sorted.270.bam.idx  sorted.35.bam.idx  sorted.6.bam.idx
sorted.0.bam             sorted.134.bam      sorted.169.bam      sorted.202.bam      sorted.237.bam      sorted.271.bam      sorted.36.bam      sorted.70.bam
sorted.0.bam.idx         sorted.134.bam.idx  sorted.169.bam.idx  sorted.202.bam.idx  sorted.237.bam.idx  sorted.271.bam.idx  sorted.36.bam.idx  sorted.70.bam.idx
sorted.100.bam           sorted.135.bam      sorted.16.bam       sorted.203.bam      sorted.238.bam      sorted.272.bam      sorted.37.bam      sorted.71.bam
sorted.100.bam.idx       sorted.135.bam.idx  sorted.16.bam.idx   sorted.203.bam.idx  sorted.238.bam.idx  sorted.272.bam.idx  sorted.37.bam.idx  sorted.71.bam.idx
sorted.101.bam           sorted.136.bam      sorted.170.bam      sorted.204.bam      sorted.239.bam      sorted.273.bam      sorted.38.bam      sorted.72.bam
sorted.101.bam.idx       sorted.136.bam.idx  sorted.170.bam.idx  sorted.204.bam.idx  sorted.239.bam.idx  sorted.273.bam.idx  sorted.38.bam.idx  sorted.72.bam.idx
sorted.102.bam           sorted.137.bam      sorted.171.bam      sorted.205.bam      sorted.23.bam       sorted.274.bam      sorted.39.bam      sorted.73.bam
sorted.102.bam.idx       sorted.137.bam.idx  sorted.171.bam.idx  sorted.205.bam.idx  sorted.23.bam.idx   sorted.274.bam.idx  sorted.39.bam.idx  sorted.73.bam.idx
sorted.103.bam           sorted.138.bam      sorted.172.bam      sorted.206.bam      sorted.240.bam      sorted.275.bam      sorted.3.bam       sorted.74.bam
sorted.103.bam.idx       sorted.138.bam.idx  sorted.172.bam.idx  sorted.206.bam.idx  sorted.240.bam.idx  sorted.275.bam.idx  sorted.3.bam.idx   sorted.74.bam.idx
sorted.104.bam           sorted.139.bam      sorted.173.bam      sorted.207.bam      sorted.241.bam      sorted.276.bam      sorted.40.bam      sorted.75.bam
sorted.104.bam.idx       sorted.139.bam.idx  sorted.173.bam.idx  sorted.207.bam.idx  sorted.241.bam.idx  sorted.276.bam.idx  sorted.40.bam.idx  sorted.75.bam.idx
sorted.105.bam           sorted.13.bam       sorted.174.bam      sorted.208.bam      sorted.242.bam      sorted.277.bam      sorted.41.bam      sorted.76.bam
sorted.105.bam.idx       sorted.13.bam.idx   sorted.174.bam.idx  sorted.208.bam.idx  sorted.242.bam.idx  sorted.277.bam.idx  sorted.41.bam.idx  sorted.76.bam.idx
sorted.106.bam           sorted.140.bam      sorted.175.bam      sorted.209.bam      sorted.243.bam      sorted.278.bam      sorted.42.bam      sorted.77.bam
sorted.106.bam.idx       sorted.140.bam.idx  sorted.175.bam.idx  sorted.209.bam.idx  sorted.243.bam.idx  sorted.278.bam.idx  sorted.42.bam.idx  sorted.77.bam.idx
sorted.107.bam           sorted.141.bam      sorted.176.bam      sorted.20.bam       sorted.244.bam      sorted.279.bam      sorted.43.bam      sorted.78.bam
sorted.107.bam.idx       sorted.141.bam.idx  sorted.176.bam.idx  sorted.20.bam.idx   sorted.244.bam.idx  sorted.279.bam.idx  sorted.43.bam.idx  sorted.78.bam.idx
sorted.108.bam           sorted.142.bam      sorted.177.bam      sorted.210.bam      sorted.245.bam      sorted.27.bam       sorted.44.bam      sorted.79.bam
sorted.108.bam.idx       sorted.142.bam.idx  sorted.177.bam.idx  sorted.210.bam.idx  sorted.245.bam.idx  sorted.27.bam.idx   sorted.44.bam.idx  sorted.79.bam.idx
sorted.109.bam           sorted.143.bam      sorted.178.bam      sorted.211.bam      sorted.246.bam      sorted.280.bam      sorted.45.bam      sorted.7.bam
sorted.109.bam.idx       sorted.143.bam.idx  sorted.178.bam.idx  sorted.211.bam.idx  sorted.246.bam.idx  sorted.280.bam.idx  sorted.45.bam.idx  sorted.7.bam.idx
sorted.10.bam            sorted.144.bam      sorted.179.bam      sorted.212.bam      sorted.247.bam      sorted.281.bam      sorted.46.bam      sorted.80.bam
sorted.10.bam.idx        sorted.144.bam.idx  sorted.179.bam.idx  sorted.212.bam.idx  sorted.247.bam.idx  sorted.281.bam.idx  sorted.46.bam.idx  sorted.80.bam.idx
sorted.110.bam           sorted.145.bam      sorted.17.bam       sorted.213.bam      sorted.248.bam      sorted.282.bam      sorted.47.bam      sorted.81.bam
sorted.110.bam.idx       sorted.145.bam.idx  sorted.17.bam.idx   sorted.213.bam.idx  sorted.248.bam.idx  sorted.282.bam.idx  sorted.47.bam.idx  sorted.81.bam.idx
sorted.111.bam           sorted.146.bam      sorted.180.bam      sorted.214.bam      sorted.249.bam      sorted.283.bam      sorted.48.bam      sorted.82.bam
sorted.111.bam.idx       sorted.146.bam.idx  sorted.180.bam.idx  sorted.214.bam.idx  sorted.249.bam.idx  sorted.283.bam.idx  sorted.48.bam.idx  sorted.82.bam.idx
sorted.112.bam           sorted.147.bam      sorted.181.bam      sorted.215.bam      sorted.24.bam       sorted.284.bam      sorted.49.bam      sorted.83.bam
sorted.112.bam.idx       sorted.147.bam.idx  sorted.181.bam.idx  sorted.215.bam.idx  sorted.24.bam.idx   sorted.284.bam.idx  sorted.49.bam.idx  sorted.83.bam.idx
sorted.113.bam           sorted.148.bam      sorted.182.bam      sorted.216.bam      sorted.250.bam      sorted.285.bam      sorted.4.bam       sorted.84.bam
sorted.113.bam.idx       sorted.148.bam.idx  sorted.182.bam.idx  sorted.216.bam.idx  sorted.250.bam.idx  sorted.285.bam.idx  sorted.4.bam.idx   sorted.84.bam.idx
sorted.114.bam           sorted.149.bam      sorted.183.bam      sorted.217.bam      sorted.251.bam      sorted.286.bam      sorted.50.bam      sorted.85.bam
sorted.114.bam.idx       sorted.149.bam.idx  sorted.183.bam.idx  sorted.217.bam.idx  sorted.251.bam.idx  sorted.286.bam.idx  sorted.50.bam.idx  sorted.85.bam.idx
sorted.115.bam           sorted.14.bam       sorted.184.bam      sorted.218.bam      sorted.252.bam      sorted.287.bam      sorted.51.bam      sorted.86.bam
sorted.115.bam.idx       sorted.14.bam.idx   sorted.184.bam.idx  sorted.218.bam.idx  sorted.252.bam.idx  sorted.287.bam.idx  sorted.51.bam.idx  sorted.86.bam.idx
sorted.116.bam           sorted.150.bam      sorted.185.bam      sorted.219.bam      sorted.253.bam      sorted.288.bam      sorted.52.bam      sorted.87.bam
sorted.116.bam.idx       sorted.150.bam.idx  sorted.185.bam.idx  sorted.219.bam.idx  sorted.253.bam.idx  sorted.288.bam.idx  sorted.52.bam.idx  sorted.87.bam.idx
sorted.117.bam           sorted.151.bam      sorted.186.bam      sorted.21.bam       sorted.254.bam      sorted.289.bam      sorted.53.bam      sorted.88.bam
sorted.117.bam.idx       sorted.151.bam.idx  sorted.186.bam.idx  sorted.21.bam.idx   sorted.254.bam.idx  sorted.289.bam.idx  sorted.53.bam.idx  sorted.88.bam.idx
sorted.118.bam           sorted.152.bam      sorted.187.bam      sorted.220.bam      sorted.255.bam      sorted.28.bam       sorted.54.bam      sorted.89.bam
sorted.118.bam.idx       sorted.152.bam.idx  sorted.187.bam.idx  sorted.220.bam.idx  sorted.255.bam.idx  sorted.28.bam.idx   sorted.54.bam.idx  sorted.89.bam.idx
sorted.119.bam           sorted.153.bam      sorted.188.bam      sorted.221.bam      sorted.256.bam      sorted.290.bam      sorted.55.bam      sorted.8.bam
sorted.119.bam.idx       sorted.153.bam.idx  sorted.188.bam.idx  sorted.221.bam.idx  sorted.256.bam.idx  sorted.290.bam.idx  sorted.55.bam.idx  sorted.8.bam.idx
sorted.11.bam            sorted.154.bam      sorted.189.bam      sorted.222.bam      sorted.257.bam      sorted.291.bam      sorted.56.bam      sorted.90.bam
sorted.11.bam.idx        sorted.154.bam.idx  sorted.189.bam.idx  sorted.222.bam.idx  sorted.257.bam.idx  sorted.291.bam.idx  sorted.56.bam.idx  sorted.90.bam.idx
sorted.120.bam           sorted.155.bam      sorted.18.bam       sorted.223.bam      sorted.258.bam      sorted.292.bam      sorted.57.bam      sorted.91.bam
sorted.120.bam.idx       sorted.155.bam.idx  sorted.18.bam.idx   sorted.223.bam.idx  sorted.258.bam.idx  sorted.292.bam.idx  sorted.57.bam.idx  sorted.91.bam.idx
sorted.121.bam           sorted.156.bam      sorted.190.bam      sorted.224.bam      sorted.259.bam      sorted.293.bam      sorted.58.bam      sorted.92.bam
sorted.121.bam.idx       sorted.156.bam.idx  sorted.190.bam.idx  sorted.224.bam.idx  sorted.259.bam.idx  sorted.293.bam.idx  sorted.58.bam.idx  sorted.92.bam.idx
sorted.122.bam           sorted.157.bam      sorted.191.bam      sorted.225.bam      sorted.25.bam       sorted.294.bam      sorted.59.bam      sorted.93.bam
sorted.122.bam.idx       sorted.157.bam.idx  sorted.191.bam.idx  sorted.225.bam.idx  sorted.25.bam.idx   sorted.294.bam.idx  sorted.59.bam.idx  sorted.93.bam.idx
sorted.123.bam           sorted.158.bam      sorted.192.bam      sorted.226.bam      sorted.260.bam      sorted.295.bam      sorted.5.bam       sorted.94.bam
sorted.123.bam.idx       sorted.158.bam.idx  sorted.192.bam.idx  sorted.226.bam.idx  sorted.260.bam.idx  sorted.295.bam.idx  sorted.5.bam.idx   sorted.94.bam.idx
sorted.124.bam           sorted.159.bam      sorted.193.bam      sorted.227.bam      sorted.261.bam      sorted.296.bam      sorted.60.bam      sorted.95.bam
sorted.124.bam.idx       sorted.159.bam.idx  sorted.193.bam.idx  sorted.227.bam.idx  sorted.261.bam.idx  sorted.296.bam.idx  sorted.60.bam.idx  sorted.95.bam.idx
sorted.125.bam           sorted.15.bam       sorted.194.bam      sorted.228.bam      sorted.262.bam      sorted.297.bam      sorted.61.bam      sorted.96.bam
sorted.125.bam.idx       sorted.15.bam.idx   sorted.194.bam.idx  sorted.228.bam.idx  sorted.262.bam.idx  sorted.297.bam.idx  sorted.61.bam.idx  sorted.96.bam.idx
sorted.126.bam           sorted.160.bam      sorted.195.bam      sorted.229.bam      sorted.263.bam      sorted.298.bam      sorted.62.bam      sorted.97.bam
sorted.126.bam.idx       sorted.160.bam.idx  sorted.195.bam.idx  sorted.229.bam.idx  sorted.263.bam.idx  sorted.298.bam.idx  sorted.62.bam.idx  sorted.97.bam.idx
sorted.127.bam           sorted.161.bam      sorted.196.bam      sorted.22.bam       sorted.264.bam      sorted.29.bam       sorted.63.bam      sorted.98.bam
sorted.127.bam.idx       sorted.161.bam.idx  sorted.196.bam.idx  sorted.22.bam.idx   sorted.264.bam.idx  sorted.29.bam.idx   sorted.63.bam.idx  sorted.98.bam.idx
sorted.128.bam           sorted.162.bam      sorted.197.bam      sorted.230.bam      sorted.265.bam      sorted.2.bam        sorted.64.bam      sorted.99.bam
sorted.128.bam.idx       sorted.162.bam.idx  sorted.197.bam.idx  sorted.230.bam.idx  sorted.265.bam.idx  sorted.2.bam.idx    sorted.64.bam.idx  sorted.99.bam.idx
sorted.129.bam           sorted.163.bam      sorted.198.bam      sorted.231.bam      sorted.266.bam      sorted.30.bam       sorted.65.bam      sorted.9.bam
sorted.129.bam.idx       sorted.163.bam.idx  sorted.198.bam.idx  sorted.231.bam.idx  sorted.266.bam.idx  sorted.30.bam.idx   sorted.65.bam.idx  sorted.9.bam.idx
sorted.12.bam            sorted.164.bam      sorted.199.bam      sorted.232.bam      sorted.267.bam      sorted.31.bam       sorted.66.bam
sorted.12.bam.idx        sorted.164.bam.idx  sorted.199.bam.idx  sorted.232.bam.idx  sorted.267.bam.idx  sorted.31.bam.idx   sorted.66.bam.idx

The log/messages:

Feb 10 19:29:46 bioinfo vmunix: [2864077.314148] ------------[ cut here ]------------
Feb 10 19:29:46 bioinfo vmunix: [2864077.314167] WARNING: CPU: 13 PID: 17291 at /build/linux-lts-xenial-lRzcrX/linux-lts-xenial-4.4.0/arch/x86/include/asm/thread_info.h:226 sigsuspend+0x6d/0x70()
Feb 10 19:29:46 bioinfo vmunix: [2864077.314170] Modules linked in: nfsv3 xt_multiport ipmi_devintf ip6t_REJECT nf_reject_ipv6 nf_log_ipv6 xt_hl ip6t_rt nf_conntrack_ipv6 nf_defrag_ipv6 ipt_REJECT nf_reject_ipv4 nf_log_ipv4 nf_log_common xt_LOG xt_limit xt_tcpudp xt_addrtype nf_conntrack_ipv4 nf_defrag_ipv4 xt_conntrack ip6table_filter ip6_tables nf_conntrack_netbios_ns nf_conntrack_broadcast nf_nat_ftp nf_nat nf_conntrack_ftp nf_conntrack iptable_filter ip_tables x_tables intel_rapl x86_pkg_temp_thermal intel_powerclamp coretemp kvm_intel kvm irqbypass crct10dif_pclmul crc32_pclmul ghash_clmulni_intel aesni_intel aes_x86_64 ipmi_ssif lrw gf128mul glue_helper ablk_helper cryptd joydev input_leds ast ttm drm_kms_helper sb_edac drm edac_core fb_sys_fops syscopyarea sysfillrect sysimgblt mei_me mei lpc_ich shpchp wmi ipmi_si 8250_fintek rfcomm ipmi_msghandler bnep bluetooth parport_pc ppdev acpi_pad mac_hid knem(OE) lp parport nfsd auth_rpcgss nfs_acl binfmt_misc nfs lockd grace sunrpc fscache rdma_ucm(OE) ib_ucm(OE) rdma_cm(OE) iw_cm(
Feb 10 19:29:46 bioinfo vmunix: onfigfs ib_ipoib(OE) ib_cm(OE) ib_umad(OE) mlx5_fpga_tools(OE) mlx5_ib(OE) mlx5_core(OE) mlxfw(OE) mlx4_ib(OE) ib_uverbs(OE) ib_core(OE) mlx4_en(OE) vxlan ip6_udp_tunnel udp_tunnel raid10 raid456 async_raid6_recov async_memcpy async_pq async_xor async_tx xor hid_generic mlx4_core(OE) igb mlx_compat(OE) usbhid mpt3sas i2c_algo_bit ahci dca raid_class hid libahci ptp scsi_transport_sas raid6_pq pps_core libcrc32c raid1 raid0 multipath linear fjes
Feb 10 19:29:46 bioinfo vmunix: [2864077.314320] CPU: 13 PID: 17291 Comm: sambamba.bak Tainted: G        W  OE   4.4.0-148-generic #174~14.04.1-Ubuntu
Feb 10 19:29:46 bioinfo vmunix: [2864077.314323] Hardware name: Sugon I840-G20/80B32-U4/H, BIOS 2.57 05/15/2018
Feb 10 19:29:46 bioinfo vmunix: [2864077.314325]  0000000000000000 ffff881d52a6fed0 ffffffff813eee37 0000000000000000
Feb 10 19:29:46 bioinfo vmunix: [2864077.314329]  ffffffff81cc5118 ffff881d52a6ff08 ffffffff810829f6 ffff8840360d0000
Feb 10 19:29:46 bioinfo vmunix: [2864077.314333]  0000000000936c01 00007efe9604d058 00007efe2a7fa6f8 00007efe96045f00
Feb 10 19:29:46 bioinfo vmunix: [2864077.314337] Call Trace:
Feb 10 19:29:46 bioinfo vmunix: [2864077.314350]  [<ffffffff813eee37>] dump_stack+0x63/0x8c
Feb 10 19:29:46 bioinfo vmunix: [2864077.314356]  [<ffffffff810829f6>] warn_slowpath_common+0x86/0xc0
Feb 10 19:29:46 bioinfo vmunix: [2864077.314359]  [<ffffffff81082aea>] warn_slowpath_null+0x1a/0x20
Feb 10 19:29:46 bioinfo vmunix: [2864077.314362]  [<ffffffff81092aed>] sigsuspend+0x6d/0x70
Feb 10 19:29:46 bioinfo vmunix: [2864077.314367]  [<ffffffff81094140>] SyS_rt_sigsuspend+0x40/0x50
Feb 10 19:29:46 bioinfo vmunix: [2864077.314378]  [<ffffffff8182d61b>] entry_SYSCALL_64_fastpath+0x22/0xcb
Feb 10 19:29:46 bioinfo vmunix: [2864077.314381] ---[ end trace 042f2041827a656c ]---

I don't know what happened, in previous, this command works normally, but sometimes it was deadlocked.

Originally posted by @dulunar in #189 (comment)

[pjotrp]

We only have a chance at fixing these issues when we get a reproducible example. Provide us with a run and examples that I can replicate and I'll take a look.

[dulunar]

We only have a chance at fixing these issues when we get a reproducible example. Provide us with a run and examples that I can replicate and I'll take a look.

The bam file is very large that I can't upload it, sorry.

[sklages]

@dulunar .. just curious. 14.04 is quite ancient. Any chance that you can try on a more recent version of Ubuntu or any other linux?