When i try to ujust update it fails at pruning. When that happens it keeps giving errors of not being able write to files for everything, most programs fail to even open.
I tired rebasing, system clean, ostree update it fails the same way.
does anyone knows how to fix this?
(sorry for the photo i cant write anything to pc after the error occurs.
I’m clueless about this, but according to:
you can view currently layered packages with:
rpm-ostree status
and then manually delete them with:
rpm-ostree uninstall <package>
Does that work?
EDIT: I saw the “1” next to “pruned images” in your photo and assumed you had only one layered package. But, looking again, I see “layers: 53”. If you actually have 53 layered packages in there, I don’t think manually deleting them is a viable option. What is your output of rpm-ostree status?
On system restart:
● ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
Digest: sha256:c6b55c7ab8a8e884d01fae5097645e7d2a5dd15e20418aad8fc604230a43f64b
Version: 44.20260629 (2026-06-29T06:39:09Z)
ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
Digest: sha256:b923f92d5a5b59eb992e269383eba2744601052da9d3d1595f76e79aa6ce2df0
Version: 44.20260608 (2026-06-08T19:16:10Z)
After trying to update:
Deployments:
ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
Digest: sha256:5496cc915c431cac9d99887a87a8185a3bf8aa2a6647e7d9cfb7e9cc796fb919
Version: 44.20260713 (2026-07-13T06:09:48Z)
Diff: 493 upgraded, 4 downgraded, 4 removed, 11 added
● ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
Digest: sha256:c6b55c7ab8a8e884d01fae5097645e7d2a5dd15e20418aad8fc604230a43f64b
Version: 44.20260629 (2026-06-29T06:39:09Z)
ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
Digest: sha256:b923f92d5a5b59eb992e269383eba2744601052da9d3d1595f76e79aa6ce2df0
Version: 44.20260608 (2026-06-08T19:16:10Z)
So if you reboot now, you should boot to the newest image? Or does it just vanish when you reboot?
It vanishes as far as i understand
After rebooting, what’s the output of the verbose rpm-ostree status?
rpm-ostree status -v
State: idle
AutomaticUpdates: disabled
Deployments:
● ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable (index: 0)
Digest: sha256:c6b55c7ab8a8e884d01fae5097645e7d2a5dd15e20418aad8fc604230a43f64b
Version: 44.20260629 (2026-06-29T06:39:09Z)
Commit: 518516b87956217f34551a9bd5749346bca3d5d150beae27e14f4771b93e9464
Staged: no
StateRoot: default
ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable (index: 1)
Digest: sha256:b923f92d5a5b59eb992e269383eba2744601052da9d3d1595f76e79aa6ce2df0
Version: 44.20260608 (2026-06-08T19:16:10Z)
Commit: c9665abef95efcabe78c996022e95f875b358684374f4fdcd718a58eabd93e15
StateRoot: default
What you get when you run rpm-ostree update in the terminal
Pulling manifest: ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
Staging deployment… done
Pruned images: 1 (layers: 53)
error: syscore cleanup: pruning: Pruning system repository: Deleting object 564db5ea89cb938f00473acd650ed15094
4a9bc62c6cc2958bf78b375e5e4296.file: unlinkat(56/4db5ea89cb938f00473acd650ed150944a9bc62c6cc2958bf78b375e5e429
6.file): Read-only file system
same error it seems
okay this might be an issue with the filesystem/btrfs which would cause it to mount itself read-only
check possible errors:
dmesg | grep -i -E “btrfs|read-only|error”
Not sure if i did it correctly (never troubleshooted linux before) but after inducing the error. Through dmesg commant i see these errors
BTRFS: Transaction aborted (error -117)
[ 201.761220] WARNING: fs/btrfs/extent-tree.c:3419 at __btrfs_free_extent.isra.0+0x78a/0xda0, CPU#0: kworker/u48:13/989
[ 201.761222] Modules linked in: uinput snd_seq_dummy snd_hrtimer evdi(O) nf_conntrack_netbios_ns nf_conntrack_broadcast nft_fib_inet nft_fib_ipv4 nft_fib_ip
v6 nft_fib nft_reject_inet nf_reject_ipv4 nf_reject_ipv6 nft_reject nft_ct nft_chain_nat nf_nat nf_conntrack nf_defrag_ipv6 nf_defrag_ipv4 nf_tables nfnetlink
qrtr sunrpc binfmt_misc snd_sof_pci_intel_tgl snd_sof_pci_intel_cnl snd_sof_intel_hda_generic soundwire_intel snd_sof_intel_hda_sdw_bpt snd_sof_intel_hda_com
mon snd_soc_hdac_hda snd_sof_intel_hda_mlink snd_sof_intel_hda soundwire_cadence snd_sof_pci snd_sof_xtensa_dsp snd_sof snd_sof_utils snd_soc_acpi_intel_match
snd_soc_acpi_intel_sdca_quirks soundwire_generic_allocation intel_rapl_msr snd_soc_sdw_utils intel_rapl_common snd_soc_acpi intel_uncore_frequency crc8 snd_h
da_codec_alc662 intel_uncore_frequency_common soundwire_bus snd_hda_codec_realtek_lib snd_soc_sdca snd_hda_codec_generic intel_tcc_cooling snd_hda_codec_atihd
mi snd_soc_avs snd_hda_codec_hdmi vfat snd_soc_hda_codec x86_pkg_temp_thermal
[ 201.761238] snd_hda_intel fat snd_hda_ext_core intel_powerclamp snd_hda_codec coretemp snd_soc_core snd_hda_core snd_intel_dspcfg snd_compress kvm_intel i
TCO_wdt snd_intel_sdw_acpi spi_nor ac97_bus mtd intel_pmc_bxt ee1004 snd_pcm_dmaengine snd_hwdep kvm snd_seq rapl snd_seq_device intel_cstate xone_dongle(O) s
nd_pcm xone_gip(O) snd_timer r8169 cfg80211 snd intel_uncore spi_intel_pci wmi_bmof i2c_i801 realtek pcspkr soundcore mei_me rfkill spi_intel i2c_smbus mei in
tel_pmc_core pmt_telemetry pmt_discovery serial_multi_instantiate pmt_class intel_pmc_ssram_telemetry acpi_pad acpi_tad joydev tcp_bbr tun zstd zram lz4hc_com
press lz4_compress overlay erofs netfs uas usb_storage amdgpu amdxcp drm_panel_backlight_quirks gpu_sched drm_buddy drm_ttm_helper ttm drm_exec nvme i2c_algo_
bit drm_suballoc_helper nvme_core nvme_keyring drm_display_helper nvme_auth ghash_clmulni_intel cec video hkdf intel_vsec intel_oc_wdt pinctrl_alderlake mxm_w
mi vfio_pci vfio_pci_core irqbypass vfio_iommu_type1 v4l2loopback(O) vfio videodev
[ 201.761261] iommufd hid_logitech_new(O) ntsync hid_fanatec(O) system76_thelio_io(O) mc hid_tmff_new(O) system76_io(O) kvmfr(O) gcadapter_oc(O) fuse wmi ff
_memless pkcs8_key_parser i2c_dev
[ 201.761265] Unloaded tainted modules: system76(O):2
[ 201.761267] CPU: 0 UID: 0 PID: 989 Comm: kworker/u48:13 Tainted: G W O 7.0.9-ogc3.2.fc44.x86_64 #1 PREEMPT(lazy)
[ 201.761268] Tainted: [W]=WARN, [O]=OOT_MODULE
[ 201.761269] Hardware name: Micro-Star International Co., Ltd. MS-7D43/MAG B660M BAZOOKA DDR4(MS-7D43), BIOS H.E0 09/14/2023
[ 201.761269] Workqueue: events_unbound btrfs_preempt_reclaim_metadata_space
[ 201.761271] RIP: 0010:__btrfs_free_extent.isra.0+0x78f/0xda0
[ 201.761273] Code: 44 24 10 e9 2f fd ff ff 4c 89 bc 24 b8 00 00 00 0f 0b f0 48 0f ba 28 02 0f 82 e3 0e 7d ff 48 8d 3d e6 79 a5 02 be 8b ff ff ff <67> 48 0f
b9 3a c6 44 24 1c 01 e9 c8 0e 7d ff 89 04 24 e8 aa 81 a6
[ 201.761274] RSP: 0000:ffffceed420ffbe8 EFLAGS: 00010246
[ 201.761275] RAX: ffff8da43b111b00 RBX: 0000000e8c02c000 RCX: 0000000000000000
[ 201.761275] RDX: 0000000000000011 RSI: 00000000ffffff8b RDI: ffffffff982cbe30
[ 201.761276] RBP: 0000000000000000 R08: 0000000000000076 R09: 0000000000000000
[ 201.761277] R10: 0000000000000002 R11: 0000000000000fff R12: 000000000026586c
[ 201.761277] R13: ffff8da428864c40 R14: ffff8da42d7c39a0 R15: 00000000000000f7
[ 201.761278] FS: 0000000000000000(0000) GS:ffff8dabc6a85000(0000) knlGS:0000000000000000
[ 201.761279] CS: 0010 DS: 0000 ES: 0000 CR0: 0000000080050033
[ 201.761279] CR2: 00007fde53977d40 CR3: 00000001c722e006 CR4: 0000000000f72ef0
[ 201.761280] PKRU: 55555554
[ 201.761280] Call Trace:
[ 201.761281]
[ 201.761282] ? btrfs_block_rsv_release+0x1d7/0x1f0
[ 201.761283] ? xa_find+0xa2/0x130
[ 201.761285] btrfs_run_delayed_refs_for_head+0x262/0x3b0
[ 201.761286] ? btrfs_select_ref_head+0xda/0x140
[ 201.761288] __btrfs_run_delayed_refs+0xb8/0x140
[ 201.761290] btrfs_run_delayed_refs+0x55/0x1d0
[ 201.761291] flush_space+0x2a8/0x2d0
[ 201.761293] ? need_preemptive_reclaim+0x178/0x1b0
[ 201.761295] btrfs_preempt_reclaim_metadata_space+0xe6/0x380
[ 201.761297] process_one_work+0x19b/0x3a0
[ 201.761299] worker_thread+0x1a6/0x310
[ 201.761300] ? __pfx_worker_thread+0x10/0x10
[ 201.761301] kthread+0xe1/0x120
[ 201.761303] ? __pfx_kthread+0x10/0x10
[ 201.761304] ret_from_fork+0x1a1/0x270
[ 201.761306] ? __pfx_kthread+0x10/0x10
[ 201.761307] ret_from_fork_asm+0x1a/0x30
[ 201.761309]
[ 201.761310] —[ end trace 0000000000000000 ]—
[ 201.761311] BTRFS: error (device nvme0n1p4 state A) in __btrfs_free_extent:3419: errno=-117 Filesystem corrupted
[ 201.761313] BTRFS info (device nvme0n1p4 state EA): forced readonly
[ 201.761315] BTRFS info (device nvme0n1p4 state EA): leaf 48345169920 gen 217380 total ptrs 129 free space 5728 owner 2
_________________________________
BTRFS critical (device nvme0n1p4 state EA): unable to find ref byte nr 62478532608 parent 0 root 258 owner 2513004 offset 0 slot 68
[ 201.761565] BTRFS error (device nvme0n1p4 state EA): failed to run delayed ref for logical 62478532608 num_bytes 1277952 type 178 action 2 ref_mod 1: -2
[ 201.761568] BTRFS: error (device nvme0n1p4 state EA) in btrfs_run_delayed_refs:2247: errno=-2 No such entry
Not sure if this will help, but have you tried rebasing to a previous version date of the version you have, and then trying again?
rebasing fails with the same error
The I have to agree with the previous comments, that it can be a BTRFS problem.
So I’m guessing the solution is to reinstall on EXT4. Strange that it worked fine for half a year
