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nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Slow process in get_vhla step #17

Closed KunFang93 closed 1 year ago

KunFang93 commented 1 year ago

Hi

I am trying to run the pipeline locally. However, the pipeline run very slow in get_vhla step. This step already took more than 5 days. I wondered if this is normal situation or the pipeline fall into some weird loop...I attached nf.log and .nextflow.log file. Thanks for your help~ nf.log nextflow.log

Best, Kun

riederd commented 1 year ago

Hi, thanks for your interest in nextNEOpi.

According your .nextflow.log the process get_vhla completed successfully.

Oct-26 14:38:02.363 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 117; name: get_vhla (Patient353_T1star); status: COMPLETED; exit: 0; error: -; workDir: /data/kun/ChenHZ_lab/Neoantigens/patient353/T1/work/22/ce89ac46b2ca9642858d62d0d9bc34]

It seems to hang at the MarkDuplicates process. Can you check the files in /data/kun/ChenHZ_lab/Neoantigens/patient353/T1/work/89/1f1771d1843dfa04c9ab2159038b5a? Is there a file named *_aligned_sort_mkdp.bam? If yes is it growing in size?

Can you see (ps -ax) if any of the following processes/programs are currently running:

sambamba
samtools
gatk --java-options ${params.JAVA_Xmx} SetNmMdAndUqTags

Thanks

KunFang93 commented 1 year ago

Hi,

Thanks for your prompt reply! I checked the files in the folder you mentioned, but there is no such *_aligned_sort_mkdp.bam file. The folder contains the following files:

(base) [kun@g1400png-ap01lp 1f1771d1843dfa04c9ab2159038b5a]$ ls
GRCh38.d1.vd1.dict  GRCh38.d1.vd1.fa  GRCh38.d1.vd1.fa.fai  Patient353_T1star_normal_DNA_aligned_uBAM_merged.bam

Yes, it looks like they are currently running. These are the output of ps -ax:

(base) [kun@g1400png-ap01lp 1f1771d1843dfa04c9ab2159038b5a]$ ps -ax
   PID TTY      STAT   TIME COMMAND
     1 ?        Ss    11:14 /usr/lib/systemd/systemd --switched-root --system --deserialize 22
     2 ?        S      0:33 [kthreadd]
     4 ?        S<     0:00 [kworker/0:0H]
     6 ?        S      0:51 [ksoftirqd/0]
     7 ?        S      1:59 [migration/0]
     8 ?        S      0:00 [rcu_bh]
     9 ?        S     39:04 [rcu_sched]
    10 ?        S<     0:00 [lru-add-drain]
    11 ?        S      1:27 [watchdog/0]
    12 ?        S      1:28 [watchdog/1]
    13 ?        S      2:01 [migration/1]
    14 ?        S      1:19 [ksoftirqd/1]
    16 ?        S<     0:00 [kworker/1:0H]
    18 ?        S      1:28 [watchdog/2]
    19 ?        S      1:58 [migration/2]
    20 ?        S      1:04 [ksoftirqd/2]
    22 ?        S<     0:00 [kworker/2:0H]
    23 ?        S      1:23 [watchdog/3]
    24 ?        S      1:56 [migration/3]
    25 ?        S      1:01 [ksoftirqd/3]
    27 ?        S<     0:00 [kworker/3:0H]
    28 ?        S      1:21 [watchdog/4]
    29 ?        S      1:57 [migration/4]
    30 ?        S      0:22 [ksoftirqd/4]
    32 ?        S<     0:00 [kworker/4:0H]
    33 ?        S      1:24 [watchdog/5]
    34 ?        S      1:59 [migration/5]
    35 ?        S      0:41 [ksoftirqd/5]
    37 ?        S<     0:00 [kworker/5:0H]
    38 ?        S      1:29 [watchdog/6]
    39 ?        S      1:56 [migration/6]
    40 ?        S      1:12 [ksoftirqd/6]
    42 ?        S<     0:00 [kworker/6:0H]
    43 ?        S      1:27 [watchdog/7]
    44 ?        S      1:55 [migration/7]
    45 ?        S      1:18 [ksoftirqd/7]
    47 ?        S<     0:00 [kworker/7:0H]
    48 ?        S      1:21 [watchdog/8]
    49 ?        S      1:55 [migration/8]
    50 ?        S      1:19 [ksoftirqd/8]
    52 ?        S<     0:00 [kworker/8:0H]
    53 ?        S      1:28 [watchdog/9]
    54 ?        S      1:53 [migration/9]
    55 ?        S      1:07 [ksoftirqd/9]
    57 ?        S<     0:00 [kworker/9:0H]
    58 ?        S      1:23 [watchdog/10]
    59 ?        S      1:54 [migration/10]
    60 ?        S      0:48 [ksoftirqd/10]
    62 ?        S<     0:00 [kworker/10:0H]
    63 ?        S      1:21 [watchdog/11]
    64 ?        S      1:53 [migration/11]
    65 ?        S      0:47 [ksoftirqd/11]
    67 ?        S<     0:00 [kworker/11:0H]
    68 ?        S      1:27 [watchdog/12]
    69 ?        S      2:16 [migration/12]
    70 ?        S      0:20 [ksoftirqd/12]
    72 ?        S<     0:00 [kworker/12:0H]
    74 ?        S      1:25 [watchdog/13]
    75 ?        S      2:12 [migration/13]
    76 ?        S      0:24 [ksoftirqd/13]
    78 ?        S<     0:00 [kworker/13:0H]
    79 ?        S      1:22 [watchdog/14]
    80 ?        S      2:08 [migration/14]
    81 ?        S      0:27 [ksoftirqd/14]
    83 ?        S<     0:00 [kworker/14:0H]
    84 ?        S      1:22 [watchdog/15]
    85 ?        S      2:10 [migration/15]
    86 ?        S      0:27 [ksoftirqd/15]
    88 ?        S<     0:00 [kworker/15:0H]
    89 ?        S      1:23 [watchdog/16]
    90 ?        S      2:10 [migration/16]
    91 ?        S      0:27 [ksoftirqd/16]
    93 ?        S<     0:00 [kworker/16:0H]
    94 ?        S      1:37 [watchdog/17]
    95 ?        S      2:10 [migration/17]
    96 ?        S      0:21 [ksoftirqd/17]
    98 ?        S<     0:00 [kworker/17:0H]
    99 ?        S      1:35 [watchdog/18]
   100 ?        S      2:09 [migration/18]
   101 ?        S      0:48 [ksoftirqd/18]
   103 ?        S<     0:00 [kworker/18:0H]
   104 ?        S      1:25 [watchdog/19]
   105 ?        S      2:06 [migration/19]
   106 ?        S      0:36 [ksoftirqd/19]
   108 ?        S<     0:00 [kworker/19:0H]
   109 ?        S      1:26 [watchdog/20]
   110 ?        S      2:01 [migration/20]
   111 ?        S      0:35 [ksoftirqd/20]
   113 ?        S<     0:00 [kworker/20:0H]
   114 ?        S      1:25 [watchdog/21]
   115 ?        S      2:05 [migration/21]
   116 ?        S      0:33 [ksoftirqd/21]
   118 ?        S<     0:00 [kworker/21:0H]
   119 ?        S      1:24 [watchdog/22]
   120 ?        S      2:07 [migration/22]
   121 ?        S      0:25 [ksoftirqd/22]
   123 ?        S<     0:00 [kworker/22:0H]
   124 ?        S      1:27 [watchdog/23]
   125 ?        S      2:10 [migration/23]
   126 ?        S      0:18 [ksoftirqd/23]
   128 ?        S<     0:00 [kworker/23:0H]
   129 ?        S      1:23 [watchdog/24]
   130 ?        S      0:17 [migration/24]
   131 ?        S      0:59 [ksoftirqd/24]
   133 ?        S<     0:00 [kworker/24:0H]
   134 ?        S      1:21 [watchdog/25]
   135 ?        S      0:26 [migration/25]
   136 ?        S      0:50 [ksoftirqd/25]
   138 ?        S<     0:00 [kworker/25:0H]
   139 ?        S      1:21 [watchdog/26]
   140 ?        S      0:24 [migration/26]
   141 ?        S      1:12 [ksoftirqd/26]
   143 ?        S<     0:00 [kworker/26:0H]
   144 ?        S      1:25 [watchdog/27]
   145 ?        S      0:18 [migration/27]
   146 ?        S      0:57 [ksoftirqd/27]
   148 ?        S<     0:00 [kworker/27:0H]
   149 ?        S      1:25 [watchdog/28]
   150 ?        S      0:17 [migration/28]
   151 ?        S      1:22 [ksoftirqd/28]
   153 ?        S<     0:00 [kworker/28:0H]
   154 ?        S      1:32 [watchdog/29]
   155 ?        S      0:17 [migration/29]
   156 ?        S      0:34 [ksoftirqd/29]
   158 ?        S<     0:00 [kworker/29:0H]
   159 ?        S      1:29 [watchdog/30]
   160 ?        S      0:16 [migration/30]
   161 ?        S      0:45 [ksoftirqd/30]
   163 ?        S<     0:00 [kworker/30:0H]
   164 ?        S      1:23 [watchdog/31]
   165 ?        S      0:17 [migration/31]
   166 ?        S      0:47 [ksoftirqd/31]
   168 ?        S<     0:00 [kworker/31:0H]
   169 ?        S      1:22 [watchdog/32]
   170 ?        S      0:17 [migration/32]
   171 ?        S      0:50 [ksoftirqd/32]
   173 ?        S<     0:00 [kworker/32:0H]
   174 ?        S      1:21 [watchdog/33]
   175 ?        S      0:17 [migration/33]
   176 ?        S      0:47 [ksoftirqd/33]
   178 ?        S<     0:00 [kworker/33:0H]
   179 ?        S      1:20 [watchdog/34]
   180 ?        S      0:17 [migration/34]
   181 ?        S      0:49 [ksoftirqd/34]
   183 ?        S<     0:00 [kworker/34:0H]
   184 ?        S      1:21 [watchdog/35]
   185 ?        S      0:17 [migration/35]
   186 ?        S      0:37 [ksoftirqd/35]
   188 ?        S<     0:00 [kworker/35:0H]
   189 ?        S      1:25 [watchdog/36]
   190 ?        S      0:15 [migration/36]
   191 ?        S      0:24 [ksoftirqd/36]
   193 ?        S<     0:00 [kworker/36:0H]
   194 ?        S      1:24 [watchdog/37]
   195 ?        S      0:32 [migration/37]
   196 ?        S      0:45 [ksoftirqd/37]
   198 ?        S<     0:00 [kworker/37:0H]
   199 ?        S      1:20 [watchdog/38]
   200 ?        S      0:25 [migration/38]
   201 ?        S      0:41 [ksoftirqd/38]
   203 ?        S<     0:00 [kworker/38:0H]
   204 ?        S      1:22 [watchdog/39]
   205 ?        S      0:18 [migration/39]
   206 ?        S      0:28 [ksoftirqd/39]
   208 ?        S<     0:00 [kworker/39:0H]
   209 ?        S      1:21 [watchdog/40]
   210 ?        S      0:17 [migration/40]
   211 ?        S      0:21 [ksoftirqd/40]
   213 ?        S<     0:00 [kworker/40:0H]
   214 ?        S      1:22 [watchdog/41]
   215 ?        S      0:17 [migration/41]
   216 ?        S      0:19 [ksoftirqd/41]
   218 ?        S<     0:00 [kworker/41:0H]
   219 ?        S      1:31 [watchdog/42]
   220 ?        S      0:16 [migration/42]
   221 ?        S      0:51 [ksoftirqd/42]
   223 ?        S<     0:00 [kworker/42:0H]
   224 ?        S      1:27 [watchdog/43]
   225 ?        S      0:16 [migration/43]
   226 ?        S      0:37 [ksoftirqd/43]
   228 ?        S<     0:00 [kworker/43:0H]
   229 ?        S      1:25 [watchdog/44]
   230 ?        S      0:16 [migration/44]
   231 ?        S      0:34 [ksoftirqd/44]
   233 ?        S<     0:00 [kworker/44:0H]
   234 ?        S      1:27 [watchdog/45]
   235 ?        S      0:16 [migration/45]
   236 ?        S      0:39 [ksoftirqd/45]
   238 ?        S<     0:00 [kworker/45:0H]
   239 ?        S      1:23 [watchdog/46]
   240 ?        S      0:16 [migration/46]
   241 ?        S      0:23 [ksoftirqd/46]
   243 ?        S<     0:00 [kworker/46:0H]
   244 ?        S      1:21 [watchdog/47]
   245 ?        S      0:16 [migration/47]
   246 ?        S      0:12 [ksoftirqd/47]
   248 ?        S<     0:00 [kworker/47:0H]
   251 ?        S      0:00 [kdevtmpfs]
   252 ?        S<     0:00 [netns]
   253 ?        S      0:52 [khungtaskd]
   254 ?        S<     0:00 [writeback]
   255 ?        S<     0:00 [kintegrityd]
   256 ?        S<     0:00 [bioset]
   257 ?        S<     0:00 [bioset]
   258 ?        S<     0:00 [bioset]
   259 ?        S<     0:00 [kblockd]
   261 ?        S<     0:00 [md]
   262 ?        S<     0:00 [edac-poller]
   263 ?        S<     0:00 [watchdogd]
   270 ?        S    444:39 [kswapd0]
   271 ?        S    227:36 [kswapd1]
   272 ?        SN     0:00 [ksmd]
   273 ?        SN     1:59 [khugepaged]
   274 ?        S<     0:00 [crypto]
   282 ?        S<     0:00 [kthrotld]
   285 ?        S<     0:00 [kmpath_rdacd]
   286 ?        S<     0:00 [kaluad]
   289 ?        S<     0:00 [kpsmoused]
   292 ?        S<     0:00 [ipv6_addrconf]
   306 ?        S<     0:00 [deferwq]
   362 ?        S      0:18 [kauditd]
   595 ?        S<     0:00 [nfit]
   643 ?        S<     0:00 [ata_sff]
   644 ?        S      0:00 [kworker/35:1]
   651 ?        S      0:00 [scsi_eh_0]
   652 ?        S<     0:00 [scsi_tmf_0]
   655 ?        S<     0:00 [ixgbe]
  1011 ?        S      0:00 [scsi_eh_1]
  1015 ?        S<     0:00 [scsi_tmf_1]
  1024 ?        S      0:00 [scsi_eh_2]
  1025 ?        S<     0:00 [scsi_tmf_2]
  1029 ?        S      0:00 [scsi_eh_3]
  1034 ?        S<     0:00 [scsi_tmf_3]
  1050 ?        S      0:00 [scsi_eh_4]
  1065 ?        S<     0:00 [scsi_tmf_4]
  1093 ?        S      0:00 [scsi_eh_5]
  1110 ?        S<     0:00 [scsi_tmf_5]
  1125 ?        S      0:00 [scsi_eh_6]
  1126 ?        S<     0:00 [scsi_tmf_6]
  1181 ?        S<     0:00 [ttm_swap]
  1486 ?        S<     0:00 [poll_megasas0_s]
  1511 ?        S      0:00 [scsi_eh_7]
  1512 ?        S<     0:00 [scsi_tmf_7]
  1513 ?        S      0:00 [scsi_eh_8]
  1514 ?        S<     0:00 [scsi_tmf_8]
  1515 ?        S      0:00 [scsi_eh_9]
  1516 ?        S<     0:00 [scsi_tmf_9]
  1517 ?        S      0:00 [scsi_eh_10]
  1519 ?        S<     0:00 [scsi_tmf_10]
  1520 ?        S      0:00 [scsi_eh_11]
  1521 ?        S<     0:00 [scsi_tmf_11]
  1522 ?        S      0:00 [scsi_eh_12]
  1523 ?        S<     0:00 [scsi_tmf_12]
  1524 ?        S      0:00 [scsi_eh_13]
  1525 ?        S<     0:00 [scsi_tmf_13]
  1526 ?        S      0:00 [scsi_eh_14]
  1527 ?        S<     0:00 [scsi_tmf_14]
  1627 ?        S<     0:00 [bioset]
  1628 ?        S<     0:00 [bioset]
  1629 ?        S      3:09 [md1_raid1]
  1630 ?        S<     0:00 [bioset]
  1631 ?        S<     0:00 [bioset]
  1633 ?        S      0:44 [md0_raid1]
  1634 ?        S<     2:55 [kworker/0:1H]
  1635 ?        S<     7:21 [kworker/16:1H]
  1636 ?        S<     0:00 [bioset]
  1637 ?        S<     0:00 [bioset]
  1638 ?        S    1459:40 [md2_raid1]
  1647 ?        S<     4:35 [kworker/1:1H]
  1651 ?        S      0:00 [nv_queue]
  1652 ?        S      0:00 [nv_queue]
  1653 ?        S      0:00 [nvidia-modeset/]
  1654 ?        S      0:00 [nvidia-modeset/]
  1699 ?        S      4:43 [jbd2/md2-8]
  1700 ?        S<     0:00 [ext4-rsv-conver]
  1763 ?        S<     2:50 [kworker/5:1H]
  1792 ?        Ss     4:59 /usr/lib/systemd/systemd-journald
  1804 ?        S<     0:00 [rpciod]
  1805 ?        S<     0:00 [xprtiod]
  1814 ?        Ss     0:00 /usr/sbin/lvmetad -f
  1825 ?        S<     6:32 [kworker/15:1H]
  1837 ?        Ss     0:03 /usr/lib/systemd/systemd-udevd
  1839 ?        S<     1:48 [kworker/3:1H]
  1841 ?        S<     2:29 [kworker/2:1H]
  2072 ?        S<     0:55 [kworker/4:1H]
  2073 ?        S<     6:39 [kworker/23:1H]
  2074 ?        S<     6:50 [kworker/12:1H]
  2077 ?        SN     0:00 [kipmi0]
  2082 ?        S      0:00 [irq/316-mei_me]
  2165 ?        S<     0:00 [kvm-irqfd-clean]
  3038 ?        S     56:52 [jbd2/sda1-8]
  3053 ?        S<     0:00 [ext4-rsv-conver]
  3103 ?        S<     0:00 [kworker/45:1H]
  3105 ?        S<     0:00 [kworker/39:1H]
  3121 ?        S      0:00 [jbd2/md0-8]
  3122 ?        S<     0:00 [ext4-rsv-conver]
  3425 ?        S<     6:34 [kworker/13:1H]
  3426 ?        S<sl   1:05 /sbin/auditd
  3428 ?        S<sl   1:33 /sbin/audispd
  3430 ?        S<     0:38 /usr/sbin/sedispatch
  3433 ?        Ss     0:00 /usr/sbin/rpc.idmapd
  3455 ?        Ss     0:42 /sbin/rpcbind -w
  3456 ?        Ssl  102:26 /usr/libexec/udisks2/udisksd
  3463 ?        Ss    17:32 /usr/bin/dbus-daemon --system --address=systemd: --nofork --nopidfile --systemd-activation
  3465 ?        S      0:34 /usr/sbin/chronyd
  3472 ?        Ss   418:11 /usr/sbin/irqbalance --foreground
  3474 ?        Ss     0:00 /usr/sbin/abrtd -d -s
  3476 ?        Ss   140:28 /sbin/rngd -f
  3479 ?        Ssl    0:34 /usr/sbin/gssproxy -D
  3485 ?        Ssl   17:36 /usr/lib/polkit-1/polkitd --no-debug
  3486 ?        Ss     0:32 /sbin/mdadm --monitor --scan -f --pid-file=/var/run/mdadm/mdadm.pid
  3502 ?        Ss     1:11 /usr/bin/lsmd -d
  3508 ?        Ss     0:00 /usr/bin/abrt-watch-log -F Backtrace /var/log/Xorg.0.log -- /usr/bin/abrt-dump-xorg -xD
  3538 ?        Ss     0:05 /usr/sbin/smartd -n -q never
  3539 ?        S<     6:31 [kworker/18:1H]
  3546 ?        Ss     4:28 /usr/lib/systemd/systemd-logind
  3547 ?        Ss     0:49 /usr/bin/abrt-watch-log -F BUG: WARNING: at WARNING: CPU: INFO: possible recursive locking detected ernel BUG at list_del corruption lis
  3548 ?        Ss     0:47 avahi-daemon: running [g1400png-ap01lp.local]
  3551 ?        Ssl    2:21 /usr/libexec/accounts-daemon
  3552 ?        S      0:00 avahi-daemon: chroot helper
  3553 ?        Ssl    1:10 /usr/sbin/ModemManager
  3559 ?        SNsl   9:08 /usr/libexec/rtkit-daemon
  3573 ?        Ss     0:00 /usr/sbin/mcelog --ignorenodev --daemon --syslog
  3617 ?        Ssl    2:15 /usr/sbin/NetworkManager --no-daemon
  3620 ?        S     95:26 /bin/bash /usr/sbin/ksmtuned
  3746 ?        S<     6:32 [kworker/20:1H]
  3782 ?        S<     0:34 [kworker/27:1H]
  4036 ?        Ssl   47:28 /usr/bin/python2 -Es /usr/sbin/tuned -l -P
  4038 ?        Ss     0:00 /usr/sbin/cupsd -f
  4043 ?        Ss     0:01 /usr/sbin/sshd -D
  4045 ?        Sl     4:26 /usr/sbin/munged
  4059 ?        Ss     0:00 /usr/sbin/rpc.statd
  4066 ?        Ss     0:00 /usr/sbin/rpc.mountd
  4116 ?        Ssl    0:00 /usr/sbin/libvirtd
  4246 ?        Ss     1:21 /usr/sbin/crond -n
  4257 ?        Ss     0:00 /usr/sbin/atd -f
  4273 ?        Ssl    0:00 /usr/sbin/gdm
  4362 ?        S<     6:27 [kworker/14:1H]
  4365 ?        S<     0:00 [nfsd4_callbacks]
  4366 ?        S      0:00 [lockd]
  4373 ?        S      0:00 [nfsd]
  4374 ?        S      0:00 [nfsd]
  4375 ?        S      0:00 [nfsd]
  4376 ?        S      0:00 [nfsd]
  4377 ?        S      0:00 [nfsd]
  4378 ?        S      0:00 [nfsd]
  4379 ?        S      0:00 [nfsd]
  4380 ?        S      0:00 [nfsd]
  4595 ?        Ss     1:33 /usr/libexec/postfix/master -w
  4607 ?        S      0:21 qmgr -l -t unix -u
  4626 ?        S      0:00 /usr/sbin/dnsmasq --conf-file=/var/lib/libvirt/dnsmasq/default.conf --leasefile-ro --dhcp-script=/usr/libexec/libvirt_leaseshelper
  4627 ?        S      0:00 /usr/sbin/dnsmasq --conf-file=/var/lib/libvirt/dnsmasq/default.conf --leasefile-ro --dhcp-script=/usr/libexec/libvirt_leaseshelper
  4823 tty1     Ssl+   2:15 /usr/bin/X :0 -background none -noreset -audit 4 -verbose -auth /run/gdm/auth-for-gdm-Ul0IGh/database -seat seat0 -nolisten tcp vt1
  4939 ?        Sl     0:00 gdm-session-worker [pam/gdm-launch-environment]
  4943 ?        Ssl    1:55 /usr/libexec/gnome-session-binary --autostart /usr/share/gdm/greeter/autostart
  4948 ?        S      0:00 dbus-launch --exit-with-session /usr/libexec/gnome-session-binary --autostart /usr/share/gdm/greeter/autostart
  4949 ?        Ss     0:00 /usr/bin/dbus-daemon --fork --print-pid 5 --print-address 7 --session
  4968 ?        Sl     0:00 /usr/libexec/at-spi-bus-launcher
  4973 ?        S      0:00 /usr/bin/dbus-daemon --config-file=/usr/share/defaults/at-spi2/accessibility.conf --nofork --print-address 3
  4975 ?        Sl     0:00 /usr/libexec/at-spi2-registryd --use-gnome-session
  5032 ?        Sl   471:32 /usr/bin/gnome-shell
  5039 ?        Ssl    1:08 /usr/libexec/upowerd
  5074 ?        S<     0:02 [kworker/37:1H]
  5075 ?        S<     0:44 [kworker/30:1H]
  5076 ?        S<     6:27 [kworker/17:1H]
  5080 ?        Sl     0:00 /usr/bin/pulseaudio --start --log-target=syslog
  5174 ?        Sl     5:48 ibus-daemon --xim --panel disable
  5177 ?        Sl     0:00 /usr/libexec/ibus-dconf
  5179 ?        Sl     0:00 /usr/libexec/ibus-x11 --kill-daemon
  5183 ?        Sl     0:00 /usr/libexec/ibus-portal
  5193 ?        Sl     0:00 /usr/libexec/xdg-permission-store
  5204 ?        Ssl    1:13 /usr/libexec/boltd
  5210 ?        Sl     0:00 /usr/libexec/gsd-xsettings
  5211 ?        Ssl    6:27 /usr/libexec/packagekitd
  5213 ?        Sl     0:00 /usr/libexec/gsd-a11y-settings
  5214 ?        Sl     0:00 /usr/libexec/gsd-clipboard
  5215 ?        Sl   5860:53 /usr/libexec/gsd-color
  5218 ?        Sl     0:00 /usr/libexec/gsd-datetime
  5219 ?        Sl     0:00 /usr/libexec/gsd-housekeeping
  5220 ?        Sl     0:00 /usr/libexec/gsd-keyboard
  5221 ?        Sl     1:20 /usr/libexec/gsd-media-keys
  5224 ?        Sl     0:00 /usr/libexec/gsd-mouse
  5226 ?        Sl     1:50 /usr/libexec/gsd-power
  5227 ?        Ss     1:47 /usr/sbin/wpa_supplicant -u -f /var/log/wpa_supplicant.log -c /etc/wpa_supplicant/wpa_supplicant.conf -P /var/run/wpa_supplicant.pid
  5228 ?        Sl     0:00 /usr/libexec/gsd-print-notifications
  5231 ?        Sl     0:00 /usr/libexec/gsd-rfkill
  5232 ?        Sl     0:00 /usr/libexec/gsd-screensaver-proxy
  5238 ?        Sl     0:00 /usr/libexec/gsd-sharing
  5245 ?        Sl     0:00 /usr/libexec/gsd-smartcard
  5250 ?        Sl     0:00 /usr/libexec/gsd-sound
  5254 ?        Sl     0:00 /usr/libexec/gsd-wacom
  5288 ?        Ssl    0:00 /usr/libexec/colord
  5337 ?        Sl     0:00 /usr/libexec/ibus-engine-simple
  5355 ?        S<     0:11 [kworker/24:1H]
  5409 ?        S<     1:12 [kworker/6:1H]
  5434 ?        S<     0:22 [kworker/29:1H]
  5538 ?        S<     0:01 [kworker/38:1H]
  5581 ?        S<     0:49 [kworker/31:1H]
  5608 ?        S<     5:05 [kworker/7:1H]
  5889 ?        S      0:01 [kworker/5:0]
  6420 ?        S<     0:12 [kworker/25:1H]
  6698 ?        S<     3:28 [kworker/11:1H]
  7824 ?        S<     3:44 [kworker/8:1H]
  8055 ?        S<     3:50 [kworker/10:1H]
  8919 ?        S<     6:30 [kworker/19:1H]
  8946 ?        S<     6:30 [kworker/21:1H]
  9434 ?        S<     0:01 [kworker/40:1H]
 10657 ?        S      0:01 [kworker/22:1]
 13068 ?        S<     2:32 [kworker/9:1H]
 15431 ?        S      0:03 [kworker/1:0]
 15490 ?        S      0:00 [kworker/1:2]
 16784 ?        S<     1:08 [kworker/26:1H]
 21166 ?        S<     0:34 [kworker/28:1H]
 22340 ?        S<     6:24 [kworker/22:1H]
 25623 ?        S      0:00 [UVM global queu]
 25624 ?        S      0:00 [UVM deferred re]
 25625 ?        S      0:00 [UVM Tools Event]
 27261 ?        S<     0:00 [kworker/41:1H]
 27433 ?        S<     0:00 [kworker/42:1H]
 27434 ?        S<     0:24 [kworker/32:1H]
 27488 ?        S<     0:24 [kworker/33:1H]
 27747 ?        S<     0:00 [kworker/46:1H]
 30263 ?        S      0:00 [kworker/17:1]
 30366 ?        S      0:00 [kworker/36:0]
 31128 ?        S      0:00 [kworker/42:1]
 34761 ?        S<     0:23 [kworker/34:1H]
 35177 ?        S<     0:00 [kworker/36:1H]
 35837 ?        S      0:00 [kworker/8:2]
 36026 ?        S      0:00 [kworker/20:2]
 39073 ?        S      0:00 [kworker/2:2]
 47450 ?        D      2:57 [kworker/u544:2]
 49936 ?        S      0:00 [kworker/10:1]
 50954 ?        S      0:00 [kworker/19:1]
 54416 ?        S<     0:40 [kworker/35:1H]
 54534 ?        S<     0:03 [kworker/44:1H]
 54594 ?        S<     0:00 [kworker/43:1H]
 55446 ?        S      0:01 [kworker/43:2]
 61190 ?        Sl     5:49 lw-container eventfwd
 63998 ?        S<     0:00 [kworker/47:1H]
 67292 ?        S      0:00 [kworker/38:0]
 78212 ?        Ss     0:00 scp /data/yangbowen/chipseq/rawdata/aml_project/AML193_2_S25_L003_R1_001.fastq kun@10.248.115.73:/data/kun/Bowen/AML/raw_data/ChIP-seq
 78213 ?        S      0:00 /usr/bin/ssh -x -oForwardAgent=no -oPermitLocalCommand=no -oClearAllForwardings=yes -l kun -- 10.248.115.73 scp -t /data/kun/Bowen/AML/r
 78455 ?        S      0:00 [kworker/5:1]
 79197 ?        S      0:00 [kworker/18:1]
 82385 ?        S      0:00 [kworker/30:2]
 82589 ?        S      0:01 [kworker/34:1]
 82978 ?        S      0:01 [kworker/24:1]
 83443 ?        S      0:03 [kworker/20:1]
 84252 ?        S      0:00 [kworker/45:2]
 84740 ?        S      0:00 [kworker/16:0]
 85284 ?        S      0:00 [kworker/46:0]
 85698 ?        S      0:00 [kworker/2:0]
 86092 ?        S      0:00 [kworker/31:1]
 86701 ?        S      0:00 [kworker/22:0]
 86740 ?        S      0:00 [kworker/41:2]
 86899 ?        S      0:00 [kworker/23:1]
 88937 ?        S      0:00 [kworker/27:1]
 92199 pts/4    S      0:20 relaytool
 92200 pts/4    S      0:11 ssh -F /dev/null -o CheckHostIP no -o ServerAliveInterval 15 -o ServerAliveCountMax 8 -o StrictHostKeyChecking yes -o UserKnownHostsFile
 94497 ?        Ss     0:01 SCREEN
 94498 pts/9    Ss+    0:00 /bin/bash
 94530 ?        S      0:00 [kworker/0:2]
 94812 ?        S      0:00 /bin/bash -ue .command.run
 94833 ?        S      0:00 tee .command.out
 94834 ?        S      0:00 tee .command.err
 94835 ?        S      0:00 /bin/bash -ue .command.run
 94838 ?        Sl     0:00 Singularity runtime parent
 94858 ?        S      0:00 /bin/bash /data/kun/ChenHZ_lab/Neoantigens/patient353/T1/work/89/1f1771d1843dfa04c9ab2159038b5a/.command.run nxf_trace
 94870 ?        S<     0:00 [loop1]
 94894 ?        S      0:00 /bin/bash -ue /data/kun/ChenHZ_lab/Neoantigens/patient353/T1/work/89/1f1771d1843dfa04c9ab2159038b5a/.command.sh
 94896 ?        S     22:10 /bin/bash /data/kun/ChenHZ_lab/Neoantigens/patient353/T1/work/89/1f1771d1843dfa04c9ab2159038b5a/.command.run nxf_trace
 94903 ?        Sl    20:08 sambamba markdup -t 20 --tmpdir /tmp/Kun/nextNEOpi --hash-table-size=1048576 --overflow-list-size=1000000 --io-buffer-size=1024 Patient3
 94904 ?        S      0:00 samtools sort -@20 -m 8G -O BAM -l 0 /dev/stdin
 94905 ?        S      0:00 python /opt/conda/bin/gatk --java-options -Xmx64G SetNmMdAndUqTags --TMP_DIR /tmp/Kun/nextNEOpi -R GRCh38.d1.vd1.fa -I /dev/stdin -O Pat
 95052 ?        Sl    19:44 java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsam
 96891 ?        Sl     0:00 /opt/pbis/sbin/lwsmd --start-as-daemon
 96958 ?        Sl     6:02 lw-container lwreg
 97030 ?        Sl    62:18 lw-container eventlog
 97108 ?        Sl     9:49 lw-container netlogon
 97177 ?        Sl    28:10 lw-container lwio
 97332 ?        Sl     0:00 lw-container reapsysl
100929 ?        S      0:00 [kworker/36:2]
101032 ?        S      0:00 [kworker/39:2]
101046 ?        S      0:02 [kworker/11:2]
101057 ?        S      0:00 [kworker/24:0]
101094 ?        S      0:01 [kworker/7:2]
105064 ?        S      0:02 [kworker/15:2]
105866 ?        Sl    51:56 /usr/bin/java --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-U
106175 ?        S      0:00 [kworker/34:0]
106610 ?        S      0:00 [kworker/32:0]
107698 ?        S      0:00 [kworker/32:2]
110025 ?        Sl    12:46 lw-container gpagent
112169 ?        S      0:01 [kworker/28:1]
113273 ?        S      0:00 [kworker/27:2]
113755 ?        S      0:00 [kworker/18:0]
118828 ?        S      0:00 [kworker/45:1]
120670 ?        S      0:00 [kworker/29:2]
121556 ?        S      0:00 [kworker/11:1]
121624 ?        S      0:23 [kworker/4:1]
121822 ?        S      0:01 [kworker/3:0]
125189 ?        S      0:00 [kworker/6:0]
130091 ?        S      0:00 [kworker/30:0]
130650 ?        S      0:04 [kworker/6:2]
131024 ?        Ssl    1:27 /usr/sbin/rsyslogd -n
135917 ?        S      0:01 [kworker/14:2]
136449 ?        S      0:01 [kworker/46:1]
137480 ?        S      0:00 [kworker/29:0]
138179 ?        S      0:01 [kworker/13:2]
142836 ?        S      0:02 [kworker/47:2]
145972 ?        S      0:00 [kworker/4:2]
147175 ?        S      0:00 [kworker/40:0]
147324 ?        S      0:00 [kworker/12:1]
147325 ?        S      0:00 [kworker/17:2]
149773 ?        S      0:00 [kworker/26:2]
149928 ?        S      0:00 [kworker/21:0]
152417 ?        S      0:00 [kworker/8:0]
157872 ?        S      0:00 [kworker/16:1]
158314 ?        S      0:00 [kworker/9:0]
158536 ?        S      0:00 [kworker/44:2]
159018 ?        S      0:00 [kworker/33:2]
169365 ?        S      0:00 [kworker/42:0]
175851 ?        S      0:00 [kworker/23:0]
180445 ?        S      0:00 [kworker/25:0]
183808 ?        Ss     0:00 SCREEN
183809 pts/4    Ss     0:00 /bin/bash
184196 pts/4    S+     3:06 /usr/bin/python ./gc-ctrl.py -start /data/yufan NONE /home/yufan/.globusonline forward
184203 pts/4    S+     8:46 /usr/bin/python ./gc.py /home/yufan/.globusonline /data/yufan NONE forward
189130 ?        S      0:00 [kworker/21:2]
189781 ?        S      0:00 [kworker/14:0]
193822 ?        S      0:00 [kworker/3:2]
198354 ?        S      0:00 [kworker/31:0]
202588 ?        S      0:02 [kworker/44:0]
209623 ?        S      0:01 [kworker/38:2]
209631 ?        S      0:01 [kworker/39:0]
209632 ?        S      0:01 [kworker/41:0]
209633 ?        S      0:01 [kworker/10:2]
213849 ?        S      0:00 [kworker/13:1]
221324 ?        Ss     0:00 sshd: kun [priv]
221339 ?        R      0:00 sshd: kun@pts/0
221342 pts/0    Ss     0:00 -bash
221343 ?        S      0:00 [kworker/37:0]
225336 ?        S      0:00 [kworker/25:2]
226213 ?        S      0:00 pickup -l -t unix -u
226789 ?        S      0:07 [kworker/u545:0]
231037 ?        S      0:00 [kworker/u546:2]
232139 ?        Ss     0:00 sshd: yufan [priv]
232151 ?        S      0:00 sshd: yufan@notty
232153 ?        Ss     0:00 /usr/libexec/openssh/sftp-server
232325 ?        S      0:00 [kworker/u544:0]
232458 ?        Ss     0:00 sshd: yufan [priv]
232468 ?        S      0:00 sshd: yufan@pts/10
232469 ?        Ss     0:00 sshd: yufan [priv]
232473 pts/10   Ss+    0:00 -bash
232532 ?        S      0:00 sshd: yufan@notty
232546 ?        Ss     0:00 /usr/libexec/openssh/sftp-server
233418 ?        S      0:00 [kworker/33:1]
233846 ?        Ss     0:00 sshd: yufan [priv]
233856 ?        S      0:00 sshd: yufan@notty
233859 ?        Ss     0:00 /usr/libexec/openssh/sftp-server
235709 ?        S      0:01 [kworker/35:2]
236995 ?        Ss     0:00 SCREEN
236996 pts/1    Ss     0:00 /bin/bash
237340 pts/1    S+     0:00 python /data/yufan/biotools/gatk/gatk-4.2.6.1/gatk AddOrReplaceReadGroups I=/data/yufan/apobecs/a3a/trimgaaa/E010_11C_Tail_S28.bam O=/da
237341 pts/1    S+     0:00 tee -a runtrimgaaa2.log
237342 pts/1    Sl+   28:00 java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsam
239120 ?        S      0:00 [kworker/u544:1]
239263 ?        S      0:00 [kworker/0:1]
239554 ?        S      0:02 [kworker/u545:1]
239559 ?        S      0:00 [kworker/u546:0]
239565 ?        S      0:00 [kworker/12:2]
241691 ?        S      0:00 sleep 60
241693 pts/0    R+     0:00 ps -ax
242588 ?        S      0:02 [kworker/47:0]
244433 ?        Ss     0:00 ssh-agent -s
254803 ?        Sl    15:37 lw-container lsass
255975 ?        S      0:00 [kworker/9:2]
263501 ?        S      0:00 [kworker/40:2]
264447 ?        S      0:00 [kworker/7:1]
264843 ?        S      0:01 [kworker/19:2]
268705 ?        S      0:03 [kworker/43:0]
268781 ?        S      0:00 [kworker/15:0]
271519 ?        S      0:00 [kworker/37:2]
275678 ?        S      0:00 [kworker/26:0]
276292 ?        S      0:00 [kworker/28:2]

Thanks, Kun

riederd commented 1 year ago

see #16