SFTP breaks with create-empty-src-dirs

stavae · November 25, 2025, 9:39pm

What is the problem you are having with rclone?

Copying to/from a SFTP host to/from local breaks if using create-empty-src-dirs. Without the flag everything appears to work.

Run the command 'rclone version' and share the full output of the command.

rclone v1.71.2

os/version: ubuntu 22.04 (64 bit)
os/kernel: 5.15.0-161-generic (x86_64)
os/type: linux
os/arch: amd64
go/version: go1.25.3
go/linking: static
go/tags: none

Which cloud storage system are you using? (eg Google Drive)

SFTP; specifically:
restrict,command="rclone serve sftp --stdio /tmp/rclone-test/normal",restrict ssh-rsa <bla>

The command you were trying to run (eg `rclone copy /tmp remote:tmp`)

(maybe?) notable: /mnt/storage/merged/ is a MergerFS mount. Added --include specifiers to keep log somewhat managable (without them it still breaks)

rclone copy --transfers 1 --create-empty-src-dirs --include beun --include backup.sh /mnt/storage/merged/draw/ localTest: -vv

Please run 'rclone config redacted' and share the full output. If you get command not found, please make sure to update rclone.

[localTest]
type = sftp
host = localhost
key_file = /tmp/rclone-test/test
shell_type = unix
md5sum_command = none
sha1sum_command = none

A log from the command that you were trying to run with the `-vv` flag

Exerpt of actual errors for convenience/clarity:

59:2025/11/25 22:28:52 ERROR : backup.sh: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist
90:2025/11/25 22:28:52 ERROR : 3d/garage: Failed to update directory timestamp or metadata: SetModTime failed: file does not exist
108:2025/11/25 22:28:52 ERROR : Attempt 1/3 failed with 7 errors and: failed to set directory modtime: 2 errors: last error: SetModTime stat failed: object not found
134:2025/11/25 22:28:52 ERROR : backup.sh.e924b48f.partial: partial file rename failed: Move NewObject failed: object not found
167:2025/11/25 22:28:52 ERROR : Attempt 2/3 failed with 4 errors and: SetModTime failed: file does not exist
187:2025/11/25 22:28:52 ERROR : backup.sh: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist
234:2025/11/25 22:28:52 ERROR : 3d/garage/photos and ref: Failed to update directory timestamp or metadata: SetModTime stat failed: object not found
240:2025/11/25 22:28:52 ERROR : Attempt 3/3 failed with 3 errors and: failed to set directory modtime: SetModTime stat failed: object not found

Full log

2025/11/25 22:28:51 DEBUG : rclone: Version "v1.71.2" starting with parameters ["rclone" "copy" "--transfers" "1" "--create-empty-src-dirs" "--include" "beun" "--include" "backup.sh" "/mnt/storage/merged/draw/" "localTest:" "-vv"]
2025/11/25 22:28:51 DEBUG : Creating backend with remote "/mnt/storage/merged/draw/"
2025/11/25 22:28:51 DEBUG : Using config file from "/home/stavae/.config/rclone/rclone.conf"
2025/11/25 22:28:51 DEBUG : fs cache: renaming cache item "/mnt/storage/merged/draw/" to be canonical "/mnt/storage/merged/draw"
2025/11/25 22:28:51 DEBUG : Creating backend with remote "localTest:"
2025/11/25 22:28:51 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:48664->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: Shell type "unix" from config
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: Relative path resolved to "/"
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: Using root directory "/"
2025/11/25 22:28:52 INFO  : 3d: Making directory
2025/11/25 22:28:52 INFO  : 3d: Made directory with modification time 2025-09-14 13:47:27.500648999 +0200 CEST
2025/11/25 22:28:52 DEBUG : Added delayed dir = "3d", newDst=<nil>
2025/11/25 22:28:52 INFO  : CloneAssets: Making directory
2025/11/25 22:28:52 INFO  : CloneAssets: Made directory with modification time 2025-07-14 23:36:03.624990122 +0200 CEST
2025/11/25 22:28:52 DEBUG : Added delayed dir = "CloneAssets", newDst=<nil>
2025/11/25 22:28:52 INFO  : SharkOpener: Making directory
2025/11/25 22:28:52 INFO  : SharkOpener: Made directory with modification time 2025-11-05 16:49:40.434805517 +0100 CET
2025/11/25 22:28:52 DEBUG : Added delayed dir = "SharkOpener", newDst=<nil>
2025/11/25 22:28:52 INFO  : Vibes: Making directory
2025/11/25 22:28:52 INFO  : Vibes: Made directory with modification time 2025-08-12 23:18:16.316215814 +0200 CEST
2025/11/25 22:28:52 DEBUG : Added delayed dir = "Vibes", newDst=<nil>
2025/11/25 22:28:52 DEBUG : backup.sh: Need to transfer - File not found at Destination
2025/11/25 22:28:52 INFO  : beun: Making directory
2025/11/25 22:28:52 INFO  : beun: Made directory with modification time 2025-11-05 14:07:30.341999869 +0100 CET
2025/11/25 22:28:52 DEBUG : Added delayed dir = "beun", newDst=<nil>
2025/11/25 22:28:52 INFO  : brushes: Making directory
2025/11/25 22:28:52 INFO  : brushes: Made directory with modification time 2024-04-08 14:15:39 +0200 CEST
2025/11/25 22:28:52 DEBUG : Added delayed dir = "brushes", newDst=<nil>
2025/11/25 22:28:52 INFO  : cast: Making directory
2025/11/25 22:28:52 INFO  : cast: Made directory with modification time 2025-11-23 14:17:00.960136219 +0100 CET
2025/11/25 22:28:52 DEBUG : Added delayed dir = "cast", newDst=<nil>
2025/11/25 22:28:52 INFO  : learning: Making directory
2025/11/25 22:28:52 INFO  : learning: Made directory with modification time 2024-03-18 12:13:12.696999984 +0100 CET
2025/11/25 22:28:52 DEBUG : Added delayed dir = "learning", newDst=<nil>
2025/11/25 22:28:52 INFO  : ref: Making directory
2025/11/25 22:28:52 INFO  : ref: Made directory with modification time 2024-10-26 21:41:06.658885473 +0200 CEST
2025/11/25 22:28:52 DEBUG : Added delayed dir = "ref", newDst=<nil>
2025/11/25 22:28:52 INFO  : synced: Making directory
2025/11/25 22:28:52 INFO  : synced: Made directory with modification time 2025-11-25 14:38:45.049224208 +0100 CET
2025/11/25 22:28:52 DEBUG : Added delayed dir = "synced", newDst=<nil>
2025/11/25 22:28:52 INFO  : tattoo: Making directory
2025/11/25 22:28:52 INFO  : tattoo: Made directory with modification time 2025-03-08 19:59:33.996735349 +0100 CET
2025/11/25 22:28:52 DEBUG : Added delayed dir = "tattoo", newDst=<nil>
2025/11/25 22:28:52 INFO  : template: Making directory
2025/11/25 22:28:52 INFO  : template: Made directory with modification time 2024-03-23 01:41:47 +0100 CET
2025/11/25 22:28:52 DEBUG : Added delayed dir = "template", newDst=<nil>
2025/11/25 22:28:52 INFO  : cast/scrcpy-win64-v3.3.3: Making directory
2025/11/25 22:28:52 INFO  : synced/normal: Making directory
2025/11/25 22:28:52 INFO  : ref/kobold: Making directory
2025/11/25 22:28:52 INFO  : 3d/garage: Making directory
2025/11/25 22:28:52 INFO  : cast/scrcpy-win64-v3.3.3: Made directory with modification time 2025-11-23 14:37:15.62293118 +0100 CET
2025/11/25 22:28:52 DEBUG : Added delayed dir = "cast/scrcpy-win64-v3.3.3", newDst=<nil>
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:48668->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:48680->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/25 22:28:52 ERROR : backup.sh: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist
2025/11/25 22:28:52 INFO  : backup.sh.e924b48f.partial: Removing failed copy
2025/11/25 22:28:52 INFO  : backup.sh.e924b48f.partial: Failed to remove failed copy: remove /backup.sh.e924b48f.partial: file does not exist
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:48686->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:48688->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/25 22:28:52 INFO  : synced/normal: Made directory with modification time 2025-11-25 19:07:44.936193284 +0100 CET
2025/11/25 22:28:52 INFO  : synced/secrets: Making directory
2025/11/25 22:28:52 INFO  : synced/secrets: Made directory with modification time 2025-11-10 15:45:04.406986298 +0100 CET
2025/11/25 22:28:52 INFO  : synced/secrets/F_hR8BJC1_WlzauziWxBqw: Making directory
2025/11/25 22:28:52 INFO  : synced/secrets/F_hR8BJC1_WlzauziWxBqw/ukf2kR_OuwQRPgIntfhL-Q: Making directory
2025/11/25 22:28:52 INFO  : ref/kobold: Made directory with modification time 2024-10-26 20:06:44.431809376 +0200 CEST
2025/11/25 22:28:52 INFO  : ref/women: Making directory
2025/11/25 22:28:52 INFO  : ref/women: Made directory with modification time 2024-10-26 20:06:00.544383105 +0200 CEST
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:48696->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/25 22:28:52 INFO  : 3d/garage: Made directory with modification time 2025-03-16 12:50:06.219365326 +0100 CET
2025/11/25 22:28:52 DEBUG : Added delayed dir = "3d/garage", newDst=<nil>
2025/11/25 22:28:52 INFO  : 3d/grip: Making directory
2025/11/25 22:28:52 INFO  : 3d/grip: Made directory with modification time 2025-09-14 13:47:57.00025648 +0200 CEST
2025/11/25 22:28:52 INFO  : 3d/handle: Making directory
2025/11/25 22:28:52 INFO  : 3d/handle: Made directory with modification time 2025-09-14 13:47:57.00025648 +0200 CEST
2025/11/25 22:28:52 INFO  : 3d/logo: Making directory
2025/11/25 22:28:52 INFO  : 3d/logo: Made directory with modification time 2025-02-20 23:08:27.069086569 +0100 CET
2025/11/25 22:28:52 INFO  : 3d/garage/photos and ref: Making directory
2025/11/25 22:28:52 INFO  : 3d/garage/photos and ref: Made directory with modification time 2025-02-26 19:14:28.351867316 +0100 CET
2025/11/25 22:28:52 INFO  : 3d/garage/photos and ref/current appartment reference: Making directory
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: Waiting for checks to finish
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: Waiting for transfers to finish
2025/11/25 22:28:52 ERROR : 3d/garage: Failed to update directory timestamp or metadata: SetModTime failed: file does not exist
2025/11/25 22:28:52 INFO  : cast/scrcpy-win64-v3.3.3: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : 3d: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : cast: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : ref: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : synced: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : learning: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : template: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : tattoo: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : CloneAssets: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : Vibes: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : SharkOpener: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:48704->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:48708->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/25 22:28:52 INFO  : beun: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : brushes: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 ERROR : Attempt 1/3 failed with 7 errors and: failed to set directory modtime: 2 errors: last error: SetModTime stat failed: object not found
2025/11/25 22:28:52 DEBUG : backup.sh.e924b48f.partial: Excluded (Path Filter)
2025/11/25 22:28:52 DEBUG : backup.sh.e924b48f.partial: Excluded
2025/11/25 22:28:52 INFO  : 3d: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "3d", newDst=3d
2025/11/25 22:28:52 INFO  : CloneAssets: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "CloneAssets", newDst=CloneAssets
2025/11/25 22:28:52 INFO  : SharkOpener: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "SharkOpener", newDst=SharkOpener
2025/11/25 22:28:52 DEBUG : Vibes: Directory modification time the same (differ by -316.215814ms, within tolerance 1s)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "Vibes", newDst=Vibes
2025/11/25 22:28:52 DEBUG : backup.sh: Need to transfer - File not found at Destination
2025/11/25 22:28:52 INFO  : beun: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "beun", newDst=beun
2025/11/25 22:28:52 INFO  : brushes: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "brushes", newDst=brushes
2025/11/25 22:28:52 INFO  : cast: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "cast", newDst=cast
2025/11/25 22:28:52 INFO  : learning: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "learning", newDst=learning
2025/11/25 22:28:52 INFO  : ref: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "ref", newDst=ref
2025/11/25 22:28:52 INFO  : synced: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "synced", newDst=synced
2025/11/25 22:28:52 ERROR : backup.sh.e924b48f.partial: partial file rename failed: Move NewObject failed: object not found
2025/11/25 22:28:52 INFO  : backup.sh.e924b48f.partial: Removing failed copy
2025/11/25 22:28:52 INFO  : tattoo: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "tattoo", newDst=tattoo
2025/11/25 22:28:52 INFO  : backup.sh.e924b48f.partial: Failed to remove failed copy: remove /backup.sh.e924b48f.partial: file does not exist
2025/11/25 22:28:52 INFO  : template: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "template", newDst=template
2025/11/25 22:28:52 INFO  : ref/kobold: Making directory
2025/11/25 22:28:52 DEBUG : cast/scrcpy-win64-v3.3.3: Directory modification time the same (differ by -622.93118ms, within tolerance 1s)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "cast/scrcpy-win64-v3.3.3", newDst=cast/scrcpy-win64-v3.3.3
2025/11/25 22:28:52 INFO  : 3d/garage: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "3d/garage", newDst=3d/garage
2025/11/25 22:28:52 INFO  : ref/kobold: Made directory with modification time 2024-10-26 20:06:44.431809376 +0200 CEST
2025/11/25 22:28:52 INFO  : ref/women: Making directory
2025/11/25 22:28:52 INFO  : 3d/grip: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "3d/grip", newDst=3d/grip
2025/11/25 22:28:52 INFO  : synced/normal: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "synced/normal", newDst=synced/normal
2025/11/25 22:28:52 INFO  : ref/women: Made directory with modification time 2024-10-26 20:06:00.544383105 +0200 CEST
2025/11/25 22:28:52 INFO  : synced/secrets: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "synced/secrets", newDst=synced/secrets
2025/11/25 22:28:52 INFO  : synced/secrets/F_hR8BJC1_WlzauziWxBqw: Making directory
2025/11/25 22:28:52 INFO  : 3d/garage/photos and ref: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "3d/garage/photos and ref", newDst=3d/garage/photos and ref
2025/11/25 22:28:52 INFO  : synced/secrets/F_hR8BJC1_WlzauziWxBqw/ukf2kR_OuwQRPgIntfhL-Q: Making directory
2025/11/25 22:28:52 INFO  : 3d/garage/photos and ref/current appartment reference: Making directory
2025/11/25 22:28:52 INFO  : 3d/garage/photos and ref/current appartment reference: Made directory with modification time 2025-02-22 22:34:10.345831576 +0100 CET
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: Waiting for checks to finish
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: Waiting for transfers to finish
2025/11/25 22:28:52 ERROR : Attempt 2/3 failed with 4 errors and: SetModTime failed: file does not exist
2025/11/25 22:28:52 DEBUG : backup.sh.e924b48f.partial: Excluded (Path Filter)
2025/11/25 22:28:52 DEBUG : backup.sh.e924b48f.partial: Excluded
2025/11/25 22:28:52 INFO  : 3d: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "3d", newDst=3d
2025/11/25 22:28:52 INFO  : CloneAssets: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "CloneAssets", newDst=CloneAssets
2025/11/25 22:28:52 DEBUG : SharkOpener: Directory modification time the same (differ by -434.805517ms, within tolerance 1s)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "SharkOpener", newDst=SharkOpener
2025/11/25 22:28:52 INFO  : Vibes: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "Vibes", newDst=Vibes
2025/11/25 22:28:52 DEBUG : backup.sh: Need to transfer - File not found at Destination
2025/11/25 22:28:52 INFO  : beun: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "beun", newDst=beun
2025/11/25 22:28:52 INFO  : brushes: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "brushes", newDst=brushes
2025/11/25 22:28:52 INFO  : cast: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "cast", newDst=cast
2025/11/25 22:28:52 ERROR : backup.sh: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist
2025/11/25 22:28:52 INFO  : learning: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "learning", newDst=learning
2025/11/25 22:28:52 INFO  : backup.sh.e924b48f.partial: Removing failed copy
2025/11/25 22:28:52 INFO  : ref: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "ref", newDst=ref
2025/11/25 22:28:52 DEBUG : synced: Directory modification time the same (differ by -49.224208ms, within tolerance 1s)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "synced", newDst=synced
2025/11/25 22:28:52 INFO  : tattoo: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "tattoo", newDst=tattoo
2025/11/25 22:28:52 DEBUG : template: Directory modification time the same (differ by 0s, within tolerance 1s)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "template", newDst=template
2025/11/25 22:28:52 INFO  : cast/scrcpy-win64-v3.3.3: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "cast/scrcpy-win64-v3.3.3", newDst=cast/scrcpy-win64-v3.3.3
2025/11/25 22:28:52 INFO  : synced/normal: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "synced/normal", newDst=synced/normal
2025/11/25 22:28:52 INFO  : synced/secrets: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "synced/secrets", newDst=synced/secrets
2025/11/25 22:28:52 INFO  : 3d/garage: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "3d/garage", newDst=3d/garage
2025/11/25 22:28:52 INFO  : 3d/grip: Making directory
2025/11/25 22:28:52 INFO  : 3d/grip: Made directory with modification time 2025-09-14 13:47:57.00025648 +0200 CEST
2025/11/25 22:28:52 DEBUG : Added delayed dir = "3d/grip", newDst=<nil>
2025/11/25 22:28:52 INFO  : 3d/handle: Making directory
2025/11/25 22:28:52 INFO  : ref/kobold: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "ref/kobold", newDst=ref/kobold
2025/11/25 22:28:52 INFO  : ref/women: Making directory
2025/11/25 22:28:52 INFO  : synced/secrets/F_hR8BJC1_WlzauziWxBqw: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 DEBUG : Added delayed dir = "synced/secrets/F_hR8BJC1_WlzauziWxBqw", newDst=synced/secrets/F_hR8BJC1_WlzauziWxBqw
2025/11/25 22:28:52 INFO  : ref/women: Made directory with modification time 2024-10-26 20:06:00.544383105 +0200 CEST
2025/11/25 22:28:52 DEBUG : Added delayed dir = "ref/women", newDst=<nil>
2025/11/25 22:28:52 INFO  : synced/secrets/F_hR8BJC1_WlzauziWxBqw/ukf2kR_OuwQRPgIntfhL-Q: Making directory
2025/11/25 22:28:52 INFO  : 3d/handle: Made directory with modification time 2025-09-14 13:47:57.00025648 +0200 CEST
2025/11/25 22:28:52 INFO  : 3d/logo: Making directory
2025/11/25 22:28:52 INFO  : synced/secrets/F_hR8BJC1_WlzauziWxBqw/ukf2kR_OuwQRPgIntfhL-Q: Made directory with modification time 2025-11-09 23:05:54.696464383 +0100 CET
2025/11/25 22:28:52 INFO  : 3d/logo: Made directory with modification time 2025-02-20 23:08:27.069086569 +0100 CET
2025/11/25 22:28:52 INFO  : 3d/garage/photos and ref: Making directory
2025/11/25 22:28:52 INFO  : 3d/garage/photos and ref: Made directory with modification time 2025-02-26 19:14:28.351867316 +0100 CET
2025/11/25 22:28:52 DEBUG : Added delayed dir = "3d/garage/photos and ref", newDst=<nil>
2025/11/25 22:28:52 INFO  : 3d/garage/photos and ref/current appartment reference: Making directory
2025/11/25 22:28:52 INFO  : 3d/garage/photos and ref/current appartment reference: Made directory with modification time 2025-02-22 22:34:10.345831576 +0100 CET
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: Waiting for checks to finish
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: Waiting for transfers to finish
2025/11/25 22:28:52 ERROR : 3d/garage/photos and ref: Failed to update directory timestamp or metadata: SetModTime stat failed: object not found
2025/11/25 22:28:52 INFO  : 3d/garage: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : 3d/grip: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : ref/women: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : 3d: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 INFO  : ref: Set directory modification time (using DirSetModTime)
2025/11/25 22:28:52 ERROR : Attempt 3/3 failed with 3 errors and: failed to set directory modtime: SetModTime stat failed: object not found
2025/11/25 22:28:52 INFO  : 
Transferred:   	    3.683 KiB / 3.683 KiB, 100%, 0 B/s, ETA -
Errors:                 3 (retrying may help)
Checks:                 0 / 0, -, Listed 131
Elapsed time:         0.9s

2025/11/25 22:28:52 DEBUG : 77 go routines active
2025/11/25 22:28:52 DEBUG : sftp://stavae@localhost:22/: Closing 8 unused connections
2025/11/25 22:28:53 NOTICE: Failed to copy with 3 errors: last error was: failed to set directory modtime: SetModTime stat failed: object not found

asdffdsa · November 25, 2025, 9:55pm

welcome to the forum,

can test the sftp server without using mergerfs...

to keep the log smaller, use --retries=1

stavae · November 26, 2025, 3:04pm

Much fewer files/dirs -- no MergerFS and --retries=1; same problem

/tmp/rclone-test/source2 -- local source 
/tmp/rclone-test/a       -- empty destination (using 'restrict,command="rclone serve sftp --stdio /tmp/rclone-test/a",restrict ssh-rsa <bla>')

Result:

rclone copy -vv --retries 1 --transfers 1 --create-empty-src-dirs source2/ localTest:
2025/11/26 15:59:40 DEBUG : rclone: Version "v1.71.2" starting with parameters ["rclone" "copy" "-vv" "--retries" "1" "--transfers" "1" "--create-empty-src-dirs" "source2/" "localTest:"]
2025/11/26 15:59:40 DEBUG : Creating backend with remote "source2/"
2025/11/26 15:59:40 DEBUG : Using config file from "/home/stavae/.config/rclone/rclone.conf"
2025/11/26 15:59:40 DEBUG : fs cache: renaming cache item "source2/" to be canonical "/tmp/rclone-test/source2"
2025/11/26 15:59:40 DEBUG : Creating backend with remote "localTest:"
2025/11/26 15:59:40 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:38168->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/26 15:59:41 DEBUG : sftp://stavae@localhost:22/: Shell type "unix" from config
2025/11/26 15:59:41 DEBUG : sftp://stavae@localhost:22/: Relative path resolved to "/"
2025/11/26 15:59:41 DEBUG : sftp://stavae@localhost:22/: Using root directory "/"
2025/11/26 15:59:41 DEBUG : backup.sh: Need to transfer - File not found at Destination
2025/11/26 15:59:41 DEBUG : export-as-pngs.sh: Need to transfer - File not found at Destination
2025/11/26 15:59:41 INFO  : tattoo: Making directory
2025/11/26 15:59:41 DEBUG : backup.sh.53d3863c.partial: renamed to: backup.sh
2025/11/26 15:59:41 INFO  : backup.sh: Copied (new)
2025/11/26 15:59:41 DEBUG : export-as-pngs.sh.2e330cd2.partial: renamed to: export-as-pngs.sh
2025/11/26 15:59:41 INFO  : export-as-pngs.sh: Copied (new)
2025/11/26 15:59:41 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:38176->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/26 15:59:41 INFO  : tattoo: Made directory with modification time 2025-03-08 19:59:33.996735349 +0100 CET
2025/11/26 15:59:41 DEBUG : tattoo/blood.png: Need to transfer - File not found at Destination
2025/11/26 15:59:41 DEBUG : tattoo/blood.svg: Need to transfer - File not found at Destination
2025/11/26 15:59:41 DEBUG : tattoo/plasma.png: Need to transfer - File not found at Destination
2025/11/26 15:59:41 DEBUG : sftp://stavae@localhost:22/: Waiting for checks to finish
2025/11/26 15:59:41 DEBUG : sftp://stavae@localhost:22/: Waiting for transfers to finish
2025/11/26 15:59:41 ERROR : tattoo/blood.png: Failed to copy: Update Create failed: file does not exist
2025/11/26 15:59:41 ERROR : tattoo/blood.svg: Failed to copy: Update Create failed: file does not exist
2025/11/26 15:59:41 ERROR : tattoo/plasma.png: Failed to copy: Update Create failed: file does not exist
2025/11/26 15:59:41 ERROR : Attempt 1/1 failed with 3 errors and: Update Create failed: file does not exist
2025/11/26 15:59:41 INFO  :
Transferred:            548 B / 548 B, 100%, 0 B/s, ETA -
Errors:                 3 (retrying may help)
Checks:                 0 / 0, -, Listed 6
Transferred:            2 / 2, 100%
Elapsed time:         0.2s

2025/11/26 15:59:41 DEBUG : 24 go routines active
2025/11/26 15:59:41 DEBUG : sftp://stavae@localhost:22/: Closing 2 unused connections
2025/11/26 15:59:41 NOTICE: Failed to copy with 3 errors: last error was: Update Create failed: file does not exist

stavae · November 26, 2025, 3:06pm

Oh I also just remembered that the server is running Ubuntu 22.04.5 LTS -> rclone version available with apt was old -> I installed this version sudo -v ; curl https://rclone.org/install.sh | sudo bash

asdffdsa · November 26, 2025, 3:22pm

sorry, confused. what does it matter which rclone version is running on the server?

stavae · November 26, 2025, 4:07pm

I dont know that it does, I am just pointing out it isnt the 'standard/vetted' apt version -> weird dependency issues could happen.
But I just realized the binary is statically linked -> should not matter

ncw · November 26, 2025, 9:17pm

This does look like a bug.

The only unusual part of your setup is the restricted ssh key. Can you try it without that?

stavae · November 26, 2025, 9:29pm

No difference (yes I tripple checked I actually removed it [also I apparently have restrict in there twice for some reason])

rclone copy --retries 1 --transfers 1 --create-empty-src-dirs source2/ localTest: -vv
2025/11/26 22:26:34 DEBUG : rclone: Version "v1.71.2" starting with parameters ["rclone" "copy" "--retries" "1" "--transfers" "1" "--create-empty-src-dirs" "source2/" "localTest:" "-vv"]
2025/11/26 22:26:34 DEBUG : Creating backend with remote "source2/"
2025/11/26 22:26:34 DEBUG : Using config file from "/home/stavae/.config/rclone/rclone.conf"
2025/11/26 22:26:34 DEBUG : fs cache: renaming cache item "source2/" to be canonical "/tmp/rclone-test/source2"
2025/11/26 22:26:34 DEBUG : Creating backend with remote "localTest:"
2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:53120->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: Shell type "unix" from config
2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: Relative path resolved to "/"
2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: Using root directory "/"
2025/11/26 22:26:34 DEBUG : backup.sh: Need to transfer - File not found at Destination
2025/11/26 22:26:34 DEBUG : export-as-pngs.sh: Need to transfer - File not found at Destination
2025/11/26 22:26:34 INFO  : tattoo: Making directory
2025/11/26 22:26:34 INFO  : tattoo: Made directory with modification time 2025-03-08 19:59:33.996735349 +0100 CET
2025/11/26 22:26:34 DEBUG : Added delayed dir = "tattoo", newDst=<nil>
2025/11/26 22:26:34 DEBUG : tattoo/blood.png: Need to transfer - File not found at Destination
2025/11/26 22:26:34 DEBUG : tattoo/blood.svg: Need to transfer - File not found at Destination
2025/11/26 22:26:34 DEBUG : tattoo/plasma.png: Need to transfer - File not found at Destination
2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: Waiting for checks to finish
2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: Waiting for transfers to finish
2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:53126->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13"
2025/11/26 22:26:34 ERROR : backup.sh: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist
2025/11/26 22:26:34 INFO  : backup.sh.53d3863c.partial: Removing failed copy
2025/11/26 22:26:34 INFO  : backup.sh.53d3863c.partial: Failed to remove failed copy: remove /backup.sh.53d3863c.partial: file does not exist
2025/11/26 22:26:34 ERROR : export-as-pngs.sh: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist
2025/11/26 22:26:34 INFO  : export-as-pngs.sh.2e330cd2.partial: Removing failed copy
2025/11/26 22:26:34 INFO  : export-as-pngs.sh.2e330cd2.partial: Failed to remove failed copy: remove /export-as-pngs.sh.2e330cd2.partial: file does not exist
2025/11/26 22:26:34 ERROR : tattoo/blood.png.aacb46b3.partial: partial file rename failed: Move NewObject failed: object not found
2025/11/26 22:26:34 INFO  : tattoo/blood.png.aacb46b3.partial: Removing failed copy
2025/11/26 22:26:34 INFO  : tattoo/blood.png.aacb46b3.partial: Failed to remove failed copy: remove /tattoo/blood.png.aacb46b3.partial: file does not exist
2025/11/26 22:26:34 ERROR : tattoo/blood.svg: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist
2025/11/26 22:26:35 INFO  : tattoo/blood.svg.422e65c1.partial: Removing failed copy
2025/11/26 22:26:35 INFO  : tattoo/blood.svg.422e65c1.partial: Failed to remove failed copy: remove /tattoo/blood.svg.422e65c1.partial: file does not exist
2025/11/26 22:26:35 ERROR : tattoo/plasma.png: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist
2025/11/26 22:26:35 INFO  : tattoo/plasma.png.59132860.partial: Removing failed copy
2025/11/26 22:26:35 INFO  : tattoo/plasma.png.59132860.partial: Failed to remove failed copy: remove /tattoo/plasma.png.59132860.partial: file does not exist
2025/11/26 22:26:35 INFO  : tattoo: Set directory modification time (using DirSetModTime)
2025/11/26 22:26:35 ERROR : Attempt 1/1 failed with 5 errors and: Update SetModTime failed: SetModTime failed: file does not exist
2025/11/26 22:26:35 INFO  :
Transferred:      916.203 KiB / 916.203 KiB, 100%, 0 B/s, ETA -
Errors:                 5 (retrying may help)
Checks:                 0 / 0, -, Listed 6
Elapsed time:         0.2s

2025/11/26 22:26:35 DEBUG : 22 go routines active
2025/11/26 22:26:35 DEBUG : sftp://stavae@localhost:22/: Closing 2 unused connections
2025/11/26 22:26:35 NOTICE: Failed to copy with 5 errors: last error was: Update SetModTime failed: SetModTime failed: file does not exist

ncw · November 26, 2025, 11:14pm

Thanks for checking. Can you report this on GitHub please and we'll try to make a fix

I think it is to do with the different order that things happen with the --create-empty-src-dirs flag.

Thank you

stavae · November 26, 2025, 11:36pm

github.com/rclone/rclone

SFTP breaks with create-empty-src-dirs

opened 11:36PM - 26 Nov 25 UTC

stavae

#### The associated forum post URL from `https://forum.rclone.org` https://forum….rclone.org/t/sftp-breaks-with-create-empty-src-dirs/53047/1 #### What is the problem you are having with rclone? Copying to/from a SFTP host to/from local breaks if using create-empty-src-dirs. Without the flag everything appears to work. This issue also exists in the `bisync` command (where I first ran into it infact, using `copy` for this bugreport instead as it is much simpler) #### What is your rclone version (output from `rclone version`) ``` rclone v1.71.2 os/version: ubuntu 22.04 (64 bit) os/kernel: 5.15.0-161-generic (x86_64) os/type: linux os/arch: amd64 go/version: go1.25.3 go/linking: static go/tags: none ``` #### Which OS you are using and how many bits (e.g. Windows 7, 64 bit) `ubuntu 22.04 (64 bit)` [also tried running this from termux client, which is where i first ran into this issue; still using the Ubuntu server as a SFTP server] #### Which cloud storage system are you using? (e.g. Google Drive) Localhost via SFTP; specifically: ``` restrict,command="rclone serve sftp --stdio /tmp/rclone-test/normal",restrict ssh-rsa <bla> // Also tested; same result command="rclone serve sftp --stdio /tmp/rclone-test/normal", ssh-rsa <bla> ``` #### The command you were trying to run (e.g. `rclone copy /tmp remote:tmp`) ``` rclone copy --retries 1 --transfers 1 --create-empty-src-dirs source2/ localTest: ``` This issue also exists in the `bisync` command (where I first ran into it infact, using `copy` for this bugreport instead as it is much simpler) #### A log from the command with the `-vv` flag (e.g. output from `rclone -vv copy /tmp remote:tmp`) ``` rclone copy --retries 1 --transfers 1 --create-empty-src-dirs source2/ localTest: -vv 2025/11/26 22:26:34 DEBUG : rclone: Version "v1.71.2" starting with parameters ["rclone" "copy" "--retries" "1" "--transfers" "1" "--create-empty-src-dirs" "source2/" "localTest:" "-vv"] 2025/11/26 22:26:34 DEBUG : Creating backend with remote "source2/" 2025/11/26 22:26:34 DEBUG : Using config file from "/home/stavae/.config/rclone/rclone.conf" 2025/11/26 22:26:34 DEBUG : fs cache: renaming cache item "source2/" to be canonical "/tmp/rclone-test/source2" 2025/11/26 22:26:34 DEBUG : Creating backend with remote "localTest:" 2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:53120->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13" 2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: Shell type "unix" from config 2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: Relative path resolved to "/" 2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: Using root directory "/" 2025/11/26 22:26:34 DEBUG : backup.sh: Need to transfer - File not found at Destination 2025/11/26 22:26:34 DEBUG : export-as-pngs.sh: Need to transfer - File not found at Destination 2025/11/26 22:26:34 INFO : tattoo: Making directory 2025/11/26 22:26:34 INFO : tattoo: Made directory with modification time 2025-03-08 19:59:33.996735349 +0100 CET 2025/11/26 22:26:34 DEBUG : Added delayed dir = "tattoo", newDst=<nil> 2025/11/26 22:26:34 DEBUG : tattoo/blood.png: Need to transfer - File not found at Destination 2025/11/26 22:26:34 DEBUG : tattoo/blood.svg: Need to transfer - File not found at Destination 2025/11/26 22:26:34 DEBUG : tattoo/plasma.png: Need to transfer - File not found at Destination 2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: Waiting for checks to finish 2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: Waiting for transfers to finish 2025/11/26 22:26:34 DEBUG : sftp://stavae@localhost:22/: New connection 127.0.0.1:53126->127.0.0.1:22 to "SSH-2.0-OpenSSH_8.9p1 Ubuntu-3ubuntu0.13" 2025/11/26 22:26:34 ERROR : backup.sh: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist 2025/11/26 22:26:34 INFO : backup.sh.53d3863c.partial: Removing failed copy 2025/11/26 22:26:34 INFO : backup.sh.53d3863c.partial: Failed to remove failed copy: remove /backup.sh.53d3863c.partial: file does not exist 2025/11/26 22:26:34 ERROR : export-as-pngs.sh: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist 2025/11/26 22:26:34 INFO : export-as-pngs.sh.2e330cd2.partial: Removing failed copy 2025/11/26 22:26:34 INFO : export-as-pngs.sh.2e330cd2.partial: Failed to remove failed copy: remove /export-as-pngs.sh.2e330cd2.partial: file does not exist 2025/11/26 22:26:34 ERROR : tattoo/blood.png.aacb46b3.partial: partial file rename failed: Move NewObject failed: object not found 2025/11/26 22:26:34 INFO : tattoo/blood.png.aacb46b3.partial: Removing failed copy 2025/11/26 22:26:34 INFO : tattoo/blood.png.aacb46b3.partial: Failed to remove failed copy: remove /tattoo/blood.png.aacb46b3.partial: file does not exist 2025/11/26 22:26:34 ERROR : tattoo/blood.svg: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist 2025/11/26 22:26:35 INFO : tattoo/blood.svg.422e65c1.partial: Removing failed copy 2025/11/26 22:26:35 INFO : tattoo/blood.svg.422e65c1.partial: Failed to remove failed copy: remove /tattoo/blood.svg.422e65c1.partial: file does not exist 2025/11/26 22:26:35 ERROR : tattoo/plasma.png: Failed to copy: Update SetModTime failed: SetModTime failed: file does not exist 2025/11/26 22:26:35 INFO : tattoo/plasma.png.59132860.partial: Removing failed copy 2025/11/26 22:26:35 INFO : tattoo/plasma.png.59132860.partial: Failed to remove failed copy: remove /tattoo/plasma.png.59132860.partial: file does not exist 2025/11/26 22:26:35 INFO : tattoo: Set directory modification time (using DirSetModTime) 2025/11/26 22:26:35 ERROR : Attempt 1/1 failed with 5 errors and: Update SetModTime failed: SetModTime failed: file does not exist 2025/11/26 22:26:35 INFO : Transferred: 916.203 KiB / 916.203 KiB, 100%, 0 B/s, ETA - Errors: 5 (retrying may help) Checks: 0 / 0, -, Listed 6 Elapsed time: 0.2s 2025/11/26 22:26:35 DEBUG : 22 go routines active 2025/11/26 22:26:35 DEBUG : sftp://stavae@localhost:22/: Closing 2 unused connections 2025/11/26 22:26:35 NOTICE: Failed to copy with 5 errors: last error was: Update SetModTime failed: SetModTime failed: file does not exist ``` #### How to use GitHub * Please use the 👍 [reaction](https://blog.github.com/2016-03-10-add-reactions-to-pull-requests-issues-and-comments/) to show that you are affected by the same issue. * Please don't comment if you have no relevant information to add. It's just extra noise for everyone subscribed to this issue. * Subscribe to receive notifications on status change and new comments.

SFTP breaks with create-empty-src-dirs

What is the problem you are having with rclone?

Run the command 'rclone version' and share the full output of the command.

Which cloud storage system are you using? (eg Google Drive)

The command you were trying to run (eg rclone copy /tmp remote:tmp)

Please run 'rclone config redacted' and share the full output. If you get command not found, please make sure to update rclone.

A log from the command that you were trying to run with the -vv flag

The command you were trying to run (eg `rclone copy /tmp remote:tmp`)

A log from the command that you were trying to run with the `-vv` flag