Fedora 39 boots into dracut emergency shell

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One day, I uninstalled some Flatpaks and reinstalled them in the /home directory. Then the next day, I booted into Fedora and it got me to dracut’s emergency shell. It generated an ‘rdsosreport.txt` file, which can be found here.

I was told that the whole Flatpak thing probably has nothing to do with the issue, but I mentioned to make sure you have a complete picture. The same issue happens on both kernels I have (6.6.7-200 & 6.5.6-300), as well as the rescue version. Can this be troubleshooted?

Thanks for any help!

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[    1.825114] fedora systemd-fsck[455]: /dev/sdd6 contains a file system with errors, check forced.
[    1.840610] fedora kernel: usb 1-4: New USB device found, idVendor=0781, idProduct=5567, bcdDevice= 1.00
[    1.840614] fedora kernel: usb 1-4: New USB device strings: Mfr=1, Product=2, SerialNumber=3
[    1.840615] fedora kernel: usb 1-4: Product: Cruzer Blade
[    1.840616] fedora kernel: usb 1-4: Manufacturer: SanDisk
[    1.840617] fedora kernel: usb 1-4: SerialNumber: 03025801051123014401
[    1.913288] fedora systemd-fsck[455]: /dev/sdd6: Inode 40913 seems to contain garbage.
[    1.913288] fedora systemd-fsck[455]: /dev/sdd6: UNEXPECTED INCONSISTENCY; RUN fsck MANUALLY.
[    1.913288] fedora systemd-fsck[455]: 	(i.e., without -a or -p options)
[    1.922501] fedora systemd-fsck[451]: fsck failed with exit status 4.
[    1.923134] fedora systemd[1]: systemd-fsck-root.service: Main process exited, code=exited, status=1/FAILURE
[    1.923255] fedora systemd[1]: systemd-fsck-root.service: Failed with result 'exit-code'.
[    1.929227] fedora systemd[1]: Failed to start systemd-fsck-root.service - File System Check on /dev/disk/by-uuid/66178548-51cf-451c-915c-12b112193eb4.
[    1.929293] fedora systemd[1]: Dependency failed for sysroot.mount - /sysroot.
[    1.929318] fedora systemd[1]: Dependency failed for initrd-root-fs.target - Initrd Root File System.
[    1.929335] fedora systemd[1]: Dependency failed for initrd-parse-etc.service - Mountpoints Configured in the Real Root.
[    1.929356] fedora systemd[1]: initrd-parse-etc.service: Job initrd-parse-etc.service/start failed with result 'dependency'.
[    1.929373] fedora systemd[1]: initrd-parse-etc.service: Triggering OnFailure= dependencies.
[    1.929480] fedora systemd[1]: initrd-root-fs.target: Job initrd-root-fs.target/start failed with result 'dependency'.
[    1.929498] fedora systemd[1]: initrd-root-fs.target: Triggering OnFailure= dependencies.
[    1.929555] fedora systemd[1]: sysroot.mount: Job sysroot.mount/start failed with result 'dependency'.
[    1.931683] fedora systemd[1]: Stopped target basic.target - Basic System.
[    1.931724] fedora systemd[1]: Reached target initrd-fs.target - Initrd File Systems.
[    1.931758] fedora systemd[1]: Stopped target sysinit.target - System Initialization.
[    1.931791] fedora systemd[1]: dracut-initqueue.service: Deactivated successfully.
[    1.937138] fedora systemd[1]: Stopped dracut-initqueue.service - dracut initqueue hook.
[    1.937275] fedora systemd[1]: dracut-pre-udev.service: Deactivated successfully.
[    1.945378] fedora systemd[1]: Stopped dracut-pre-udev.service - dracut pre-udev hook.
[    1.945407] fedora systemd[1]: dracut-cmdline.service: Deactivated successfully.
[    1.955139] fedora systemd[1]: Stopped dracut-cmdline.service - dracut cmdline hook.
[    1.955269] fedora kernel: usb 1-9: new high-speed USB device number 6 using xhci_hcd
[    1.968241] fedora systemd[1]: Started emergency.service - Emergency Shell.
[    1.968492] fedora systemd[1]: Reached target emergency.target - Emergency Mode.
[    1.968559] fedora systemd[1]: Startup finished in 1.156s (kernel) + 0 (initrd) + 812ms (userspace) = 1.968s.

It is saying your filesystem is corrupt. You’ll need to repair your filesystem to continue booting. What filesystem is /dev/sdd6 formatted with?

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/dev/sdd6 is ext4.

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Well, if you have important data on /dev/sdd6, you might want to make a low-level backup copy of it before attempting the repair. To make a backup, you’ll need a device that is at least as large as your /dev/sdd6 partition and you can use the “dd” (disk dump) command to make the copy. If /dev/sdd6 doesn’t contain important information (e.g. it is just your “root” partition, without your home directory data, and you can reconstruct it by doing a full reinstall if necessary) you can opt to skip the backup. Beware that it is quite possible that the repair operation can fail and leave your filesystem in an even worse/less-recoverable state.

If you are brave, you can run fsck -y /dev/sdd6 and hope for the best. Be sure not to interrupt the process once it begins.

2 Likes
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/dev/sdd6 is my root partition. A few days ago I added tons of space to the home partition from a now-former partition, maybe that was related.

Did an fsck -y and it fixed everything. I was lucky it was just the root partition. Thanks!