Hello,
I tried to run the following process and got this error. I am running qiime2 on a Linux system that I have installed on an external SSD.
How do I solve this issue? Or do I just have too much data to run this process? Doing the same while using the greengenes database works fine, but I would like to compare databases.
this is my input deblur file: rep-seqs-deblur.qza (61.7 KB)
(qiime2-2021.8) anke@anke-HP-Laptop-14-ck0xxx:~/qiime2-GVP$ qiime feature-classifier classify-sklearn --i-classifier silva-138-99-515-806-nb-classifier.qza --i-reads rep-seqs-deblur.qza --o-classification silva-mafft-taxonomy.qza
Killed
(qiime2-2021.8) anke@anke-HP-Laptop-14-ck0xxx:~/qiime2-GVP$ dmesg -T | grep -E -i -B100 'killed process'
[ma jan 17 20:17:54 2022] [ 717] 0 717 62636 246 114688 0 0 accounts-daemon
[ma jan 17 20:17:54 2022] [ 718] 0 718 637 17 49152 0 0 acpid
[ma jan 17 20:17:54 2022] [ 721] 115 721 2134 82 57344 0 0 avahi-daemon
[ma jan 17 20:17:54 2022] [ 722] 0 722 2092 100 57344 1 0 bluetoothd
[ma jan 17 20:17:54 2022] [ 723] 0 723 4514 54 61440 0 0 cron
[ma jan 17 20:17:54 2022] [ 725] 0 725 9304 410 90112 0 0 cupsd
[ma jan 17 20:17:54 2022] [ 728] 103 728 2484 647 53248 0 -900 dbus-daemon
[ma jan 17 20:17:54 2022] [ 729] 0 729 86877 874 159744 0 0 NetworkManager
[ma jan 17 20:17:54 2022] [ 735] 0 735 20477 82 61440 1 0 irqbalance
[ma jan 17 20:17:54 2022] [ 737] 0 737 11992 2057 118784 0 0 networkd-dispat
[ma jan 17 20:17:54 2022] [ 739] 0 739 63458 1231 118784 0 0 polkitd
[ma jan 17 20:17:54 2022] [ 741] 104 741 56089 391 81920 0 0 rsyslogd
[ma jan 17 20:17:54 2022] [ 744] 0 744 323848 3224 294912 0 -900 snapd
[ma jan 17 20:17:54 2022] [ 746] 0 746 61061 142 90112 1 0 switcheroo-cont
[ma jan 17 20:17:54 2022] [ 750] 0 750 4188 260 73728 3 0 systemd-logind
[ma jan 17 20:17:54 2022] [ 752] 0 752 33726 207 102400 0 0 thermald
[ma jan 17 20:17:54 2022] [ 760] 0 760 98898 686 131072 0 0 udisksd
[ma jan 17 20:17:54 2022] [ 762] 0 762 3485 218 69632 0 0 wpa_supplicant
[ma jan 17 20:17:54 2022] [ 766] 115 766 2088 82 57344 0 0 avahi-daemon
[ma jan 17 20:17:54 2022] [ 814] 0 814 44631 413 122880 0 0 cups-browsed
[ma jan 17 20:17:54 2022] [ 816] 7 816 3834 200 69632 0 0 dbus
[ma jan 17 20:17:54 2022] [ 818] 7 818 3834 199 69632 0 0 dbus
[ma jan 17 20:17:54 2022] [ 819] 7 819 3834 200 73728 0 0 dbus
[ma jan 17 20:17:54 2022] [ 821] 0 821 78439 419 110592 0 0 ModemManager
[ma jan 17 20:17:54 2022] [ 844] 0 844 31602 2039 135168 0 0 unattended-upgr
[ma jan 17 20:17:54 2022] [ 871] 0 871 62063 295 94208 0 0 gdm3
[ma jan 17 20:17:54 2022] [ 946] 111 946 38235 59 57344 0 0 rtkit-daemon
[ma jan 17 20:17:54 2022] [ 1064] 0 1064 65242 343 110592 0 0 upowerd
[ma jan 17 20:17:54 2022] [ 1139] 120 1139 63401 495 126976 0 0 whoopsie
[ma jan 17 20:17:54 2022] [ 1142] 116 1142 2816 102 69632 11 0 kerneloops
[ma jan 17 20:17:54 2022] [ 1148] 116 1148 2816 112 61440 0 0 kerneloops
[ma jan 17 20:17:54 2022] [ 1369] 121 1369 64406 1345 118784 0 0 colord
[ma jan 17 20:17:54 2022] [ 1401] 0 1401 43960 355 102400 0 0 gdm-session-wor
[ma jan 17 20:17:54 2022] [ 1409] 1000 1409 4770 2 77824 562 0 systemd
[ma jan 17 20:17:54 2022] [ 1410] 1000 1410 42242 679 98304 170 0 (sd-pam)
[ma jan 17 20:17:54 2022] [ 1415] 1000 1415 307399 14 192512 1234 0 pulseaudio
[ma jan 17 20:17:54 2022] [ 1417] 1000 1417 130005 2 200704 2072 0 tracker-miner-f
[ma jan 17 20:17:54 2022] [ 1420] 1000 1420 2031 4 57344 343 0 dbus-daemon
[ma jan 17 20:17:54 2022] [ 1424] 1000 1424 62084 1 110592 252 0 gvfsd
[ma jan 17 20:17:54 2022] [ 1429] 1000 1429 95516 0 114688 283 0 gvfsd-fuse
[ma jan 17 20:17:54 2022] [ 1441] 1000 1441 62173 181 94208 66 0 gnome-keyring-d
[ma jan 17 20:17:54 2022] [ 1453] 1000 1453 81521 171 114688 231 0 gvfs-udisks2-vo
[ma jan 17 20:17:54 2022] [ 1459] 1000 1459 61128 0 102400 192 0 gvfs-goa-volume
[ma jan 17 20:17:54 2022] [ 1464] 1000 1464 138452 0 258048 1525 0 goa-daemon
[ma jan 17 20:17:54 2022] [ 1476] 1000 1476 81811 0 122880 362 0 goa-identity-se
[ma jan 17 20:17:54 2022] [ 1481] 1000 1481 81340 0 118784 281 0 gvfs-afc-volume
[ma jan 17 20:17:54 2022] [ 1487] 1000 1487 61687 0 94208 228 0 gvfs-gphoto2-vo
[ma jan 17 20:17:54 2022] [ 1491] 1000 1491 61085 0 94208 185 0 gvfs-mtp-volume
[ma jan 17 20:17:54 2022] [ 1504] 1000 1504 43164 159 90112 0 0 gdm-x-session
[ma jan 17 20:17:54 2022] [ 1506] 1000 1506 211585 8021 446464 0 0 Xorg
[ma jan 17 20:17:54 2022] [ 1521] 1000 1521 49827 428 131072 0 0 gnome-session-b
[ma jan 17 20:17:54 2022] [ 1589] 1000 1589 1510 113 45056 0 0 ssh-agent
[ma jan 17 20:17:54 2022] [ 1612] 1000 1612 77435 1 90112 261 0 at-spi-bus-laun
[ma jan 17 20:17:54 2022] [ 1617] 1000 1617 1812 1 53248 131 0 dbus-daemon
[ma jan 17 20:17:54 2022] [ 1625] 1000 1625 24675 0 77824 113 0 gnome-session-c
[ma jan 17 20:17:54 2022] [ 1632] 1000 1632 123779 2 163840 691 0 gnome-session-b
[ma jan 17 20:17:54 2022] [ 1646] 1000 1646 1115357 8375 1257472 26436 0 gnome-shell
[ma jan 17 20:17:54 2022] [ 1674] 1000 1674 99259 1 126976 406 0 ibus-daemon
[ma jan 17 20:17:54 2022] [ 1678] 1000 1678 62253 0 102400 257 0 ibus-dconf
[ma jan 17 20:17:54 2022] [ 1679] 1000 1679 71699 1 180224 3473 0 ibus-extension-
[ma jan 17 20:17:54 2022] [ 1683] 1000 1683 52272 0 176128 2534 0 ibus-x11
[ma jan 17 20:17:54 2022] [ 1685] 1000 1685 62248 0 94208 247 0 ibus-portal
[ma jan 17 20:17:54 2022] [ 1697] 1000 1697 40710 1 86016 219 0 at-spi2-registr
[ma jan 17 20:17:54 2022] [ 1701] 1000 1701 61058 0 90112 157 0 xdg-permission-
[ma jan 17 20:17:54 2022] [ 1705] 1000 1705 145466 0 196608 881 0 gnome-shell-cal
[ma jan 17 20:17:54 2022] [ 1714] 1000 1714 99773 2 204800 978 0 evolution-sourc
[ma jan 17 20:17:54 2022] [ 1721] 1000 1721 211863 0 270336 1153 0 evolution-calen
[ma jan 17 20:17:54 2022] [ 1727] 1000 1727 734787 0 274432 1347 0 gjs
[ma jan 17 20:17:54 2022] [ 1741] 1000 1741 80639 0 110592 260 0 gsd-a11y-settin
[ma jan 17 20:17:54 2022] [ 1742] 1000 1742 147358 56 229376 2517 0 gsd-color
[ma jan 17 20:17:54 2022] [ 1743] 1000 1743 95752 0 180224 565 0 gsd-datetime
[ma jan 17 20:17:54 2022] [ 1746] 1000 1746 80698 41 110592 213 0 gsd-housekeepin
[ma jan 17 20:17:54 2022] [ 1749] 1000 1749 89262 1 184320 2584 0 gsd-keyboard
[ma jan 17 20:17:54 2022] [ 1751] 1000 1751 228060 3 233472 2719 0 gsd-media-keys
[ma jan 17 20:17:54 2022] [ 1753] 1000 1753 107789 129 204800 2442 0 gsd-power
[ma jan 17 20:17:54 2022] [ 1756] 1000 1756 64214 1 122880 375 0 gsd-print-notif
[ma jan 17 20:17:54 2022] [ 1758] 1000 1758 116434 0 118784 210 0 gsd-rfkill
[ma jan 17 20:17:54 2022] [ 1759] 1000 1759 61036 0 94208 164 0 gsd-screensaver
[ma jan 17 20:17:54 2022] [ 1760] 1000 1760 119400 121 143360 306 0 gsd-sharing
[ma jan 17 20:17:54 2022] [ 1762] 1000 1762 81680 0 118784 316 0 gsd-smartcard
[ma jan 17 20:17:54 2022] [ 1763] 1000 1763 82606 0 122880 357 0 gsd-sound
[ma jan 17 20:17:54 2022] [ 1765] 1000 1765 99132 0 122880 278 0 gsd-usb-protect
[ma jan 17 20:17:54 2022] [ 1767] 1000 1767 70713 0 167936 2582 0 gsd-wacom
[ma jan 17 20:17:54 2022] [ 1774] 1000 1774 57950 0 81920 307 0 gsd-disk-utilit
[ma jan 17 20:17:54 2022] [ 1782] 1000 1782 81721 0 118784 331 0 gsd-wwan
[ma jan 17 20:17:54 2022] [ 1784] 1000 1784 89410 1 180224 2738 0 gsd-xsettings
[ma jan 17 20:17:54 2022] [ 1788] 1000 1788 180109 0 352256 4075 0 evolution-alarm
[ma jan 17 20:17:54 2022] [ 1835] 1000 1835 43796 0 94208 247 0 ibus-engine-sim
[ma jan 17 20:17:54 2022] [ 1838] 1000 1838 81549 0 118784 389 0 gvfsd-trash
[ma jan 17 20:17:54 2022] [ 1883] 1000 1883 87707 1 172032 494 0 gsd-printer
[ma jan 17 20:17:54 2022] [ 1888] 1000 1888 39058 1 73728 173 0 dconf-service
[ma jan 17 20:17:54 2022] [ 1896] 1000 1896 188953 1 253952 1008 0 evolution-addre
[ma jan 17 20:17:54 2022] [ 1963] 1000 1963 42724 0 81920 165 0 gvfsd-metadata
[ma jan 17 20:17:54 2022] [ 1966] 1000 1966 107874 125 192512 2304 0 update-notifier
[ma jan 17 20:17:54 2022] [ 2095] 1000 2095 100027 0 135168 352 0 gvfsd-network
[ma jan 17 20:17:54 2022] [ 2107] 1000 2107 80906 0 110592 287 0 gvfsd-dnssd
[ma jan 17 20:17:54 2022] [ 2208] 1000 2208 205846 362 274432 2815 0 gnome-terminal-
[ma jan 17 20:17:54 2022] [ 2216] 1000 2216 4880 11 61440 402 0 bash
[ma jan 17 20:17:54 2022] [ 2950] 1000 2950 3469220 1756947 17829888 425262 0 qiime
[ma jan 17 20:17:54 2022] oom-kill:constraint=CONSTRAINT_NONE,nodemask=(null),cpuset=/,mems_allowed=0,global_oom,task_memcg=/user.slice/user-1000.slice/[email protected],task=qiime,pid=2950,uid=1000
[ma jan 17 20:17:54 2022] Out of memory: Killed process 2950 (qiime) total-vm:13876880kB, anon-rss:7027784kB, file-rss:4kB, shmem-rss:0kB, UID:1000 pgtables:17412kB oom_score_adj:0
