I am trying to run the software MinKnow on my Linux device (ubuntu 22.04). This is a GUI based program for DNA sequence analysis, and is giving an error "Post-run basecalling is currently unavailable. Please restart your device and then try again." and "No workflows found" when I try to run my analysis.
To troubleshoot this I began by checking my nvidia drivers are installed properly, following this thread I ran:
dkms status
and I got:
nvidia/535.183.01, 5.15.0-112-generic, x86_64: installed
Based on the aforementioned thread, I concluded that I likely have the same headers issue, and proceeded to download all of the module and header .deb files from here. When I navigate to the folder they are contained in (downloads) try to run:
sudo dpkg -i *.deb
I get this output:
(Reading database ... 317785 files and directories currently installed.)
Preparing to unpack docker-desktop-4.30.0-amd64.deb ...
Unpacking docker-desktop (4.30.0-149282) over (4.30.0-149282) ...
Preparing to unpack linux-headers-6.7.2-060702_6.7.2-060702.202401251943_all.deb ...
Unpacking linux-headers-6.7.2-060702 (6.7.2-060702.202401251943) over (6.7.2-060702.202401251943) ...
Preparing to unpack linux-headers-6.7.2-060702-generic_6.7.2-060702.202401251943_amd64.deb ...
Unpacking linux-headers-6.7.2-060702-generic (6.7.2-060702.202401251943) over (6.7.2-060702.202401251943) ...
Preparing to unpack linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_amd64.deb ...
Unpacking linux-modules-6.7.2-060702-generic (6.7.2-060702.202401251943) over (6.7.2-060702.202401251943) ...
dpkg: error processing archive linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_armhf.deb (--install):
package architecture (armhf) does not match system (amd64)
dpkg: error processing archive linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_ppc64el.deb (--install):
package architecture (ppc64el) does not match system (amd64)
dpkg: error processing archive linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_s390x.deb (--install):
package architecture (s390x) does not match system (amd64)
dpkg: regarding teamviewer-host_15.54.3_amd64.deb containing teamviewer-host:
teamviewer-host conflicts with teamviewer
teamviewer (version 15.54.3) is present and installed.
dpkg: error processing archive teamviewer-host_15.54.3_amd64.deb (--install):
conflicting packages - not installing teamviewer-host
Setting up docker-desktop (4.30.0-149282) ...
Enabling use of privileged ports by Docker Desktop
kubernetes.docker.internal already in /etc/hosts
Reloading systemd daemon for logged in users
Done reloading systemd daemon for logged in users
Setting up linux-headers-6.7.2-060702 (6.7.2-060702.202401251943) ...
dpkg: dependency problems prevent configuration of linux-headers-6.7.2-060702-generic:
linux-headers-6.7.2-060702-generic depends on libc6 (>= 2.38); however:
Version of libc6:amd64 on system is 2.35-0ubuntu3.8.
dpkg: error processing package linux-headers-6.7.2-060702-generic (--install):
dependency problems - leaving unconfigured
Setting up linux-modules-6.7.2-060702-generic (6.7.2-060702.202401251943) ...
Processing triggers for mailcap (3.70+nmu1ubuntu1) ...
Processing triggers for gnome-menus (3.36.0-1ubuntu3) ...
Processing triggers for desktop-file-utils (0.26-1ubuntu3) ...
Errors were encountered while processing:
linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_armhf.deb
linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_ppc64el.deb
linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_s390x.deb
teamviewer-host_15.54.3_amd64.deb
linux-headers-6.7.2-060702-generic
This has a number of errors which I am not sure how to interpret, and when I continue to run:
sudo dkms build nvidia/535.183.01
I get this:
Error! Your kernel headers for kernel 6.9.3-060903-generic cannot be found.
Please install the linux-headers-6.9.3-060903-generic package or use the --kernelsourcedir option to tell DKMS where it's located.
I found a number of options telling me to upgrade te kernel headers but when I run these I get a similar output, example command:
sudo apt install linux-generic
Output:
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
You might want to run 'apt --fix-broken install' to correct these.
The following packages have unmet dependencies.
linux-generic : Depends: linux-image-generic (= 5.15.0.112.112) but it is not going to be installed
linux-headers-6.7.2-060702-generic : Depends: libc6 (>= 2.38) but 2.35-0ubuntu3.8 is to be installed
E: Unmet dependencies. Try 'apt --fix-broken install' with no packages (or specify a solution).
I have ran:
sudo apt fix-broken install
This gives:
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Correcting dependencies... Done
The following packages were automatically installed and are no longer required:
libwpe-1.0-1 libwpebackend-fdo-1.0-1
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED
linux-headers-6.7.2-060702-generic
0 to upgrade, 0 to newly install, 1 to remove and 3 not to upgrade.
1 not fully installed or removed.
After this operation, 28.0 MB disk space will be freed.
Do you want to continue? [Y/n] y
(Reading database ... 317785 files and directories currently installed.)
Removing linux-headers-6.7.2-060702-generic (6.7.2-060702.202401251943) ...
After this I repeated:
sudo apt install linux-generic
Which now gives:
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
The following packages were automatically installed and are no longer required:
libwpe-1.0-1 libwpebackend-fdo-1.0-1
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
linux-image-5.15.0-112-generic linux-image-generic
linux-modules-5.15.0-112-generic linux-modules-extra-5.15.0-112-generic
Suggested packages:
fdutils linux-doc | linux-source-5.15.0 linux-tools
The following NEW packages will be installed
linux-generic linux-image-5.15.0-112-generic linux-image-generic
linux-modules-5.15.0-112-generic linux-modules-extra-5.15.0-112-generic
0 to upgrade, 5 to newly install, 0 to remove and 3 not to upgrade.
Need to get 98.1 MB of archives.
After this operation, 480 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://gb.archive.ubuntu.com/ubuntu jammy-updates/main amd64 linux-modules-5.15.0-112-generic amd64 5.15.0-112.122 [22.6 MB]
Get:2 http://gb.archive.ubuntu.com/ubuntu jammy-updates/main amd64 linux-image-5.15.0-112-generic amd64 5.15.0-112.122 [11.5 MB]
Get:3 http://gb.archive.ubuntu.com/ubuntu jammy-updates/main amd64 linux-modules-extra-5.15.0-112-generic amd64 5.15.0-112.122 [63.9 MB]
Get:4 http://gb.archive.ubuntu.com/ubuntu jammy-updates/main amd64 linux-image-generic amd64 5.15.0.112.112 [2,510 B]
Get:5 http://gb.archive.ubuntu.com/ubuntu jammy-updates/main amd64 linux-generic amd64 5.15.0.112.112 [1,692 B]
Fetched 98.1 MB in 1min 35s (1,028 kB/s)
Selecting previously unselected package linux-modules-5.15.0-112-generic.
(Reading database ... 307611 files and directories currently installed.)
Preparing to unpack .../linux-modules-5.15.0-112-generic_5.15.0-112.122_amd64.de
b ...
Unpacking linux-modules-5.15.0-112-generic (5.15.0-112.122) ...
Selecting previously unselected package linux-image-5.15.0-112-generic.
Preparing to unpack .../linux-image-5.15.0-112-generic_5.15.0-112.122_amd64.deb
...
Unpacking linux-image-5.15.0-112-generic (5.15.0-112.122) ...
Selecting previously unselected package linux-modules-extra-5.15.0-112-generic.
Preparing to unpack .../linux-modules-extra-5.15.0-112-generic_5.15.0-112.122_am
d64.deb ...
Unpacking linux-modules-extra-5.15.0-112-generic (5.15.0-112.122) ...
Selecting previously unselected package linux-image-generic.
Preparing to unpack .../linux-image-generic_5.15.0.112.112_amd64.deb ...
Unpacking linux-image-generic (5.15.0.112.112) ...
Selecting previously unselected package linux-generic.
Preparing to unpack .../linux-generic_5.15.0.112.112_amd64.deb ...
Unpacking linux-generic (5.15.0.112.112) ...
Setting up linux-image-5.15.0-112-generic (5.15.0-112.122) ...
I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.5.0-41-generic
I: /boot/initrd.img.old is now a symlink to initrd.img-6.5.0-41-generic
I: /boot/vmlinuz is now a symlink to vmlinuz-5.15.0-112-generic
I: /boot/initrd.img is now a symlink to initrd.img-5.15.0-112-generic
Setting up linux-modules-extra-5.15.0-112-generic (5.15.0-112.122) ...
Setting up linux-modules-5.15.0-112-generic (5.15.0-112.122) ...
Setting up linux-image-generic (5.15.0.112.112) ...
Setting up linux-generic (5.15.0.112.112) ...
Processing triggers for linux-image-5.15.0-112-generic (5.15.0-112.122) ...
/etc/kernel/postinst.d/dkms:
* dkms: running auto installation service for kernel 5.15.0-112-generic
...done.
/etc/kernel/postinst.d/initramfs-tools:
update-initramfs: Generating /boot/initrd.img-5.15.0-112-generic
/etc/kernel/postinst.d/zz-update-grub:
Sourcing file `/etc/default/grub'
Sourcing file `/etc/default/grub.d/init-select.cfg'
Generating grub configuration file ...
Found linux image: /boot/vmlinuz-6.9.3-060903-generic
Found initrd image: /boot/initrd.img-6.9.3-060903-generic
Found linux image: /boot/vmlinuz-6.5.0-41-generic
Found initrd image: /boot/initrd.img-6.5.0-41-generic
Found linux image: /boot/vmlinuz-6.5.0-35-generic
Found initrd image: /boot/initrd.img-6.5.0-35-generic
Found linux image: /boot/vmlinuz-5.15.0-112-generic
Found initrd image: /boot/initrd.img-5.15.0-112-generic
Memtest86+ needs a 16-bit boot, that is not available on EFI, exiting
Warning: os-prober will not be executed to detect other bootable partitions.
Systems on them will not be added to the GRUB boot configuration.
Check GRUB_DISABLE_OS_PROBER documentation entry.
Adding boot menu entry for UEFI Firmware Settings ...
done
When I now return to:
sudo dpkg -i *.deb
I get a similar output:
(Reading database ... 314838 files and directories currently installed.)
Preparing to unpack docker-desktop-4.30.0-amd64.deb ...
Unpacking docker-desktop (4.30.0-149282) over (4.30.0-149282) ...
Preparing to unpack linux-headers-6.7.2-060702_6.7.2-060702.202401251943_all.deb ...
Unpacking linux-headers-6.7.2-060702 (6.7.2-060702.202401251943) over (6.7.2-060702.202401251943) ...
Selecting previously unselected package linux-headers-6.7.2-060702-generic.
Preparing to unpack linux-headers-6.7.2-060702-generic_6.7.2-060702.202401251943_amd64.deb ...
Unpacking linux-headers-6.7.2-060702-generic (6.7.2-060702.202401251943) ...
Preparing to unpack linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_amd64.deb ...
Unpacking linux-modules-6.7.2-060702-generic (6.7.2-060702.202401251943) over (6.7.2-060702.202401251943) ...
dpkg: error processing archive linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_armhf.deb (--install):
package architecture (armhf) does not match system (amd64)
dpkg: error processing archive linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_ppc64el.deb (--install):
package architecture (ppc64el) does not match system (amd64)
dpkg: error processing archive linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_s390x.deb (--install):
package architecture (s390x) does not match system (amd64)
dpkg: regarding teamviewer-host_15.54.3_amd64.deb containing teamviewer-host:
teamviewer-host conflicts with teamviewer
teamviewer (version 15.54.3) is present and installed.
dpkg: error processing archive teamviewer-host_15.54.3_amd64.deb (--install):
conflicting packages - not installing teamviewer-host
Setting up docker-desktop (4.30.0-149282) ...
Enabling use of privileged ports by Docker Desktop
kubernetes.docker.internal already in /etc/hosts
Reloading systemd daemon for logged in users
Done reloading systemd daemon for logged in users
Setting up linux-headers-6.7.2-060702 (6.7.2-060702.202401251943) ...
dpkg: dependency problems prevent configuration of linux-headers-6.7.2-060702-generic:
linux-headers-6.7.2-060702-generic depends on libc6 (>= 2.38); however:
Version of libc6:amd64 on system is 2.35-0ubuntu3.8.
dpkg: error processing package linux-headers-6.7.2-060702-generic (--install):
dependency problems - leaving unconfigured
Setting up linux-modules-6.7.2-060702-generic (6.7.2-060702.202401251943) ...
Processing triggers for mailcap (3.70+nmu1ubuntu1) ...
Processing triggers for gnome-menus (3.36.0-1ubuntu3) ...
Processing triggers for desktop-file-utils (0.26-1ubuntu3) ...
Errors were encountered while processing:
linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_armhf.deb
linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_ppc64el.deb
linux-modules-6.7.2-060702-generic_6.7.2-060702.202401251943_s390x.deb
teamviewer-host_15.54.3_amd64.deb
linux-headers-6.7.2-060702-generic
and when I run
sudo dkms build nvidia/535.183.01
it still gives
Error! Your kernel headers for kernel 6.9.3-060903-generic cannot be found.
Please install the linux-headers-6.9.3-060903-generic package or use the --kernelsourcedir option to tell DKMS where it's located.
I am a little stuck for what I should be doing here, I think I still need to resolve the headers issue bit I am not sure what I need to do. can anyone help?
