Nautilus doesn't open initially but after a long time it starts working fine

I recently moved from 16.04 to 18.04. When I login to the system no files are shown on the desktop and 'file' icon also doesn't open. When I ran the command time nautilus it gave the following response:

Failed to register: Timeout was reached
real 0m25.074s
user 0m0.042s
sys 0m0.025s

But after 5 minutes all the windows suddenly open and folder in the desktop also start showing up. The response of the same command is as follows:

real 0m0.060s
user 0m0.038s
sys 0m0.008s

Although, I can access all the files and folder using terminal. Also, it works fine even after I issue the command nautilus -q and doesn't take much time. It seems like the problem is only when I login to the system. Although this was not the case with ubuntu 16.04 where everything started instantaneously.

Edit: I removed and installed nautilus again but no help.

Output of free -h

 total used free shared buff/cache available
Mem: 7.6G 2.7G 1.4G 268M 3.5G 4.3G
Swap: 0B 0B 0B

Output of sysctl vm.swappiness

vm.swappiness = 60

Output of ls -al ~/.local/share/gnome-shell/extensions

ls: cannot access '/home/bhavy/.local/share/gnome-shell/extensions': No such file or directory

Output of ls -al /usr/share/gnome-shell/extensions

total 16
drwxr-xr-x 4 root root 4096 Jun 7 01:52 .
drwxr-xr-x 6 root root 4096 Jun 7 01:17 ..
drwxr-xr-x 3 root root 4096 Jun 7 01:52
drwxr-xr-x 3 root root 4096 Jun 7 01:52 

Output of cat /var/log/syslog|grep nautilus

Jun 7 18:22:41 bhavy-HP whoopsie[1956]: [18:22:41] Parsing /var/crash/_usr_bin_nautilus.1000.crash.
Jun 7 18:22:41 bhavy-HP whoopsie[1956]: [18:22:41] Uploading /var/crash/_usr_bin_nautilus.1000.crash.
Jun 7 18:30:30 bhavy-HP nautilus-deskto[4472]: can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied
Jun 7 18:30:30 bhavy-HP nautilus-deskto[4472]: message repeated 2 times: [ can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied]
Jun 7 18:30:30 bhavy-HP nautilus[4565]: can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied
Jun 7 18:30:30 bhavy-HP nautilus-deskto[4472]: can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied
Jun 7 18:30:31 bhavy-HP nautilus-deskto[4472]: message repeated 44 times: [ can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied]
Jun 7 18:30:31 bhavy-HP dbus-daemon[1403]: [system] Activating via systemd: service name='org.freedesktop.hostname1' unit='dbus-org.freedesktop.hostname1.service' requested by ':1.269' (uid=1000 pid=4565 comm="/usr/bin/nautilus --gapplication-service " label="unconfined")
Jun 7 18:30:31 bhavy-HP nautilus[4565]: can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied
Jun 7 18:30:31 bhavy-HP nautilus[4565]: can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied
Jun 7 18:30:31 bhavy-HP nautilus[4565]: can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied
Jun 7 18:30:31 bhavy-HP nautilus-deskto[4472]: can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied
Jun 7 18:30:31 bhavy-HP nautilus-deskto[4472]: message repeated 191 times: [ can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied]
Jun 7 18:30:32 bhavy-HP nautilus[4565]: can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied
Jun 7 18:30:33 bhavy-HP nautilus[4565]: message repeated 129 times: [ can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied]
Jun 7 18:30:37 bhavy-HP nautilus-deskto[4472]: can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied
Jun 7 18:30:38 bhavy-HP nautilus-deskto[4472]: message repeated 143 times: [ can't init metadata tree /home/bhavy/.local/share/gvfs-metadata/home: open: Permission denied]

There was one system program error detected window as well. When I looked at the /var/crash folder with ls. It gave the following output

_usr_bin_nautilus.1000.crash _usr_bin_nautilus.1000.upload _usr_bin_nautilus.1000.uploaded

Edit 2: The following two commands sudo grep -i swap /etc/fstab and sudo blkid | grep -i swap prints nothing.

For ls -al /home/bhavy/.local/share/gvfs-metadata/ the output is

drwx------ 2 bhavy bhavy 4096 Apr 1 13:47 .
drwx------ 37 bhavy bhavy 4096 Jun 7 19:32 ..
-rw------- 1 root root 90096 Apr 14 2018 home
-rw-r--r-- 1 root root 32768 Apr 14 2018 home-520671b4.log
-rw------- 1 bhavy bhavy 1068 May 10 2018 'mtp:host=%5Busb%3A001%2C004%5D'
-rw-rw-r-- 1 bhavy bhavy 32768 May 10 2018 'mtp:host=%5Busb%3A001%2C004%5D-ea794164.log'
-rw------- 1 bhavy bhavy 892 Apr 1 13:47 'mtp:host=%5Busb%3A001%2C006%5D'
-rw-rw-r-- 1 bhavy bhavy 32768 Apr 1 13:50 'mtp:host=%5Busb%3A001%2C006%5D-96429231.log'
-rw------- 1 bhavy bhavy 1904 Mar 17 14:49 'mtp:host=%5Busb%3A001%2C008%5D'
-rw-rw-r-- 1 bhavy bhavy 32768 Mar 17 14:49 'mtp:host=%5Busb%3A001%2C008%5D-1ef4e927.log'
-rw------- 1 bhavy bhavy 988 Jan 3 2018 'mtp:host=%5Busb%3A001%2C019%5D'
-rw-rw-r-- 1 bhavy bhavy 32768 Jan 3 2018 'mtp:host=%5Busb%3A001%2C019%5D-295b34d0.log'
-rw------- 1 root root 23428 Apr 20 2018 root
-rw-r--r-- 1 root root 32768 Apr 20 2018 root-a7cd5a51.log
-rw------- 1 bhavy bhavy 528 Oct 16 2019 'sftp:host=172.27.28.229,user=jatindev'
-rw-rw-r-- 1 bhavy bhavy 32768 Oct 16 2019 'sftp:host=172.27.28.229,user=jatindev-50511b70.log'
-rw------- 1 bhavy bhavy 360 Jun 28 2018 uuid-13F2-1B57
-rw-rw-r-- 1 bhavy bhavy 32768 Jun 28 2018 uuid-13F2-1B57-ef6bea9f.log
-rw------- 1 bhavy bhavy 152 Dec 15 2017 uuid-15F6-1853
-rw-rw-r-- 1 bhavy bhavy 32768 Dec 15 2017 uuid-15F6-1853-dd280f53.log
-rw------- 1 bhavy bhavy 168 Feb 5 2019 uuid-1CB5-2250
-rw-rw-r-- 1 bhavy bhavy 32768 Feb 5 2019 uuid-1CB5-2250-57328334.log
-rw------- 1 bhavy bhavy 3652 Oct 14 2019 uuid-2E18-2B51
-rw-rw-r-- 1 bhavy bhavy 32768 Oct 14 2019 uuid-2E18-2B51-148fcb14.log
-rw------- 1 bhavy bhavy 7444 Jan 1 2019 uuid-70F1-3FAB
-rw-rw-r-- 1 bhavy bhavy 32768 Jan 1 2019 uuid-70F1-3FAB-80580a55.log
-rw------- 1 bhavy bhavy 3036 Mar 4 2018 uuid-858A-D414
-rw-rw-r-- 1 bhavy bhavy 32768 Mar 4 2018 uuid-858A-D414-6d31293d.log
-rw------- 1 bhavy bhavy 716 Aug 6 2018 uuid-CC63-C4D1
-rw-rw-r-- 1 bhavy bhavy 32768 Aug 6 2018 uuid-CC63-C4D1-86f630c5.log

Edit 3: After allocating swap memory and changing ownership of gvfs-metadata Output of free -h

 total used free shared buff/cache available
Mem: 7.6G 2.1G 3.0G 221M 2.5G 5.1G
Swap: 4.0G 0B 4.0G

Output of ls -al /home/bhavy/.local/share/gvfs-metadata/

total 716
drwx------ 2 bhavy bhavy 4096 Jun 7 20:12 .
drwx------ 37 bhavy bhavy 4096 Jun 7 20:12 ..
-rw------- 1 bhavy bhavy 90096 Apr 14 2018 home
-rw-r--r-- 1 bhavy bhavy 32768 Jun 7 20:12 home-520671b4.log
-rw------- 1 bhavy bhavy 95220 Jun 7 20:12 home.AQPML0
-rw------- 1 bhavy bhavy 1068 May 10 2018 'mtp:host=%5Busb%3A001%2C004%5D'
-rw-rw-r-- 1 bhavy bhavy 32768 May 10 2018 'mtp:host=%5Busb%3A001%2C004%5D-ea794164.log'
-rw------- 1 bhavy bhavy 892 Apr 1 13:47 'mtp:host=%5Busb%3A001%2C006%5D'
-rw-rw-r-- 1 bhavy bhavy 32768 Apr 1 13:50 'mtp:host=%5Busb%3A001%2C006%5D-96429231.log'
-rw------- 1 bhavy bhavy 1904 Mar 17 14:49 'mtp:host=%5Busb%3A001%2C008%5D'
-rw-rw-r-- 1 bhavy bhavy 32768 Mar 17 14:49 'mtp:host=%5Busb%3A001%2C008%5D-1ef4e927.log'
-rw------- 1 bhavy bhavy 988 Jan 3 2018 'mtp:host=%5Busb%3A001%2C019%5D'
-rw-rw-r-- 1 bhavy bhavy 32768 Jan 3 2018 'mtp:host=%5Busb%3A001%2C019%5D-295b34d0.log'
-rw------- 1 root root 23428 Apr 20 2018 root
-rw-r--r-- 1 root root 32768 Apr 20 2018 root-a7cd5a51.log
-rw------- 1 bhavy bhavy 528 Oct 16 2019 'sftp:host=172.27.28.229,user=jatindev'
-rw-rw-r-- 1 bhavy bhavy 32768 Oct 16 2019 'sftp:host=172.27.28.229,user=jatindev-50511b70.log'
-rw------- 1 bhavy bhavy 360 Jun 28 2018 uuid-13F2-1B57
-rw-rw-r-- 1 bhavy bhavy 32768 Jun 28 2018 uuid-13F2-1B57-ef6bea9f.log
-rw------- 1 bhavy bhavy 152 Dec 15 2017 uuid-15F6-1853
-rw-rw-r-- 1 bhavy bhavy 32768 Dec 15 2017 uuid-15F6-1853-dd280f53.log
-rw------- 1 bhavy bhavy 168 Feb 5 2019 uuid-1CB5-2250
-rw-rw-r-- 1 bhavy bhavy 32768 Feb 5 2019 uuid-1CB5-2250-57328334.log
-rw------- 1 bhavy bhavy 3652 Oct 14 2019 uuid-2E18-2B51
-rw-rw-r-- 1 bhavy bhavy 32768 Oct 14 2019 uuid-2E18-2B51-148fcb14.log
-rw------- 1 bhavy bhavy 7444 Jan 1 2019 uuid-70F1-3FAB
-rw-rw-r-- 1 bhavy bhavy 32768 Jan 1 2019 uuid-70F1-3FAB-80580a55.log
-rw------- 1 bhavy bhavy 3036 Mar 4 2018 uuid-858A-D414
-rw-rw-r-- 1 bhavy bhavy 32768 Mar 4 2018 uuid-858A-D414-6d31293d.log
-rw------- 1 bhavy bhavy 716 Aug 6 2018 uuid-CC63-C4D1
-rw-rw-r-- 1 bhavy bhavy 32768 Aug 6 2018 uuid-CC63-C4D1-86f630c5.log

1 Answer

swap

You have no swap, as seen in free -h.

 total used free shared buff/cache available
Mem: 7.6G 2.7G 1.4G 268M 3.5G 4.3G
Swap: 0B 0B 0B

We'll create a 4G /swapfile.

Note: Incorrect use of the dd command can cause data loss. Suggest copy/paste.

sudo swapoff -a # turn off swap
sudo rm -i /swapfile # remove old /swapfile
sudo dd if=/dev/zero of=/swapfile bs=1M count=4096
sudo chmod 600 /swapfile # set proper file protections
sudo mkswap /swapfile # init /swapfile
sudo swapon /swapfile # turn on swap
free -h # confirm 8G RAM and 4G swap

Add this line to /etc/fstab...

/swapfile    none    swap    sw      0 0

Then reboot and verify proper swap operation.

gvfs-metadata

You've been starting nautilus with sudo. You should be using sudo -H when starting GUI apps as root from the terminal.

sudo chown bhavy:bhavy /home/bhavy/.local/share/gvfs-metadata/home*
sudo chmod 664 /home/bhavy/.local/share/gvfs-metadata/home*.log
sudo rm -i /home/bhavy/.local/share/gvfs-metadata/root*

desktop-icons

Reinstall missing gnome-shell extension:

sudo apt-get update
sudo apt-get install gnome-shell-extension-desktop-icons

Go to to enable/configure Desktop Icons.

~/.cache

We found corruption in the ~/.cache folder. Recreated a new folder and Files now works.