[Borgbackup] Data integrity error: Invalid segment entry size 0 - too small

[Michael Siepmann]

I've been using borgbackup for a while without problems but now have an issue I'm unsure how to fix despite looking through the documentation. I'd very much appreciate any help anyone can offer. The two symptoms of the problem are that the backup used to take only a few minutes but now takes over an hour, and that the log shows a data integrity error. 

Below is an abbreviated copy of the log, noting where I've edited out large numbers of similar lines:

Many thanks in advance,

Michael Siepmann

---

Creating archive at "/mnt/synology/Qubes-personal::{hostname}-{now:%Y-%m-%d_T%H:%M}"
Synchronizing chunks cache...
Archives: 1026, w/ cached Idx: 0, w/ outdated Idx: 0, w/o cached Idx: 1026.
Fetching and building archive index for personal-2017-09-30_T16:00 ...
Merging into master chunks index ...
Fetching and building archive index for personal-2017-10-31_T22:00 ...

  <editing out many similar instances...>

Merging into master chunks index ...
Fetching and building archive index for personal-2019-03-01_T07:52 ...
Merging into master chunks index ...
Done.
------------------------------------------------------------------------------
Archive name: personal-2019-03-06_T07:28
Archive fingerprint: 76673c3396fc9ee3f74f927b75e0c7ce0c8d76c7b953469a09c160d2d827fc12
Time (start): Wed, 2019-03-06 07:28:18
Time (end):   Wed, 2019-03-06 08:15:13
Duration: 46 minutes 55.46 seconds
Number of files: 169474
Utilization of max. archive size: 0%
------------------------------------------------------------------------------
		       Original size	  Compressed size    Deduplicated size
This archive:		   109.52 GB		 91.18 GB	       3.15 GB
All archives:		   108.63 TB		 90.24 TB	     335.80 GB

		       Unique chunks	     Total chunks
Chunk index:		      510924		211576111
------------------------------------------------------------------------------
Keeping archive: personal-2019-03-06_T07:28	      Wed, 2019-03-06 07:28:18 [76673c3396fc9ee3f74f927b75e0c7ce0c8d76c7b953469a09c160d2d827fc12]
 
   <editing out several similar instances...>

Keeping archive: personal-2019-02-14_T12:00	      Thu, 2019-02-14 12:00:10 [720753a98c0b33243dd8f1407ea54159833af9691ae4324f1f7ad6149205c1aa]
Pruning archive: personal-2019-02-14_T10:00	      Thu, 2019-02-14 10:00:13 [08cf1a86db65c55cfeeecaab1c6977f7f2baf37e8c6c9803ca3334bd26b9adfc] (1/981)

   <editing out many similar instances - looks like there are 981, but after it gets to 954 there's an error...>

Pruning archive: personal-2018-07-20_T15:00	      Fri, 2018-07-20 15:00:16 [7f3e8e3477faf30de92fefec41baf2243045c085b8a957b9d764a63202ad16a8] (954/981)
Data integrity error: Invalid segment entry size 0 - too small [segment 253305, offset 2331522]
Traceback (most recent call last):
  File "/usr/lib64/python3.7/site-packages/borg/archiver.py", line 4436, in main
    exit_code = archiver.run(args)
  File "/usr/lib64/python3.7/site-packages/borg/archiver.py", line 4368, in run
    return set_ec(func(args))
  File "/usr/lib64/python3.7/site-packages/borg/archiver.py", line 152, in wrapper
    return method(self, args, repository=repository, **kwargs)
  File "/usr/lib64/python3.7/site-packages/borg/archiver.py", line 1590, in do_prune
    Archive(repository, key, manifest, archive.name, cache).delete(stats, forced=args.forced)
  File "/usr/lib64/python3.7/site-packages/borg/archive.py", line 809, in delete
    chunk_decref(chunk_id, stats)
  File "/usr/lib64/python3.7/site-packages/borg/archive.py", line 786, in chunk_decref
    self.cache.chunk_decref(id, stats, wait=False)
  File "/usr/lib64/python3.7/site-packages/borg/cache.py", line 925, in chunk_decref
    self.repository.delete(id, wait=wait)
  File "/usr/lib64/python3.7/site-packages/borg/repository.py", line 1113, in delete
    size = self.io.read(segment, offset, id, read_data=False)
  File "/usr/lib64/python3.7/site-packages/borg/repository.py", line 1392, in read
    size, tag, key, data = self._read(fd, self.put_header_fmt, header, segment, offset, (TAG_PUT, ), read_data)
  File "/usr/lib64/python3.7/site-packages/borg/repository.py", line 1419, in _read
    size, segment, offset))
borg.helpers.IntegrityError: Data integrity error: Invalid segment entry size 0 - too small [segment 253305, offset 2331522]

Platform: Linux personal 4.14.74-1.pvops.qubes.x86_64 #1 SMP Mon Oct 8 17:14:24 UTC 2018 x86_64
Linux: Fedora 29 Twenty Nine
Borg: 1.1.8  Python: CPython 3.7.2
PID: 12045  CWD: /home/user/Apps/ScriptsByMMS
sys.argv: ['/usr/bin/borg', 'prune', '-v', '--list', '/mnt/synology/Qubes-personal', '--prefix', '{hostname}-', '--keep-hourly=24', '--keep-daily=7', '--keep-weekly=6', '--keep-monthly=9']
SSH_ORIGINAL_COMMAND: None