I encountered this error today. Here is the data requested.

1) duplicity cleanup -v9 --force 'sftp://__MY_SERVER__/__MY_FOLDER__' 2&>1 > 
2) 'duplicity-inc.20170609T192036Z.to.20170620T202313Z.manifest.part' the file 
causing problems
3) 'filelist' got with command echo "ls -la ." | sftp -q 
"__MY_SERVER__:/__MY_FOLDER__'" > filelist
4) 'logfile1' result of 1)

I can only add one attachment so I zipped everything.
I get the same exception also when I try to recover an folder.

** Attachment added: "The requested files"

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  AssertionError in manifest.py: assert filecount ==

Status in Duplicity:
Status in duplicity package in Ubuntu:
Status in duplicity source package in Zesty:
  Fix Released

Bug description:
  Duplicity was almost finishing a full backup to a FTP server. When I
  restarted the backup, the following error occured:

  root@MyMachine:~# duply MyProfile backup
  Start duply v1.11, time is 2016-01-26 23:38:21.
  Using profile '/root/.duply/MyProfile'.
  Using installed duplicity version 0.7.06, python 2.7.3, gpg 1.4.12 (Home: 
~/.gnupg), awk 'mawk 1.3.3 Nov 1996, Copyright (C) Michael D. Brennan', grep 
'grep (GNU grep) 2.12', bash 'GNU bash, Version 4.2.37(1)-release 
  Autoset found secret key of first GPG_KEY entry 'XXXXXXXX' for signing.
  Checking TEMP_DIR '/tmp' is a folder and writable (OK)
  Test - Encrypt to 'XXXXXXXX' & Sign with 'XXXXXXXX' (OK)
  Test - Decrypt (OK)
  Test - Compare (OK)
  Cleanup - Delete '/tmp/duply.16938.1453847902_*'(OK)

  --- Start running command PRE at 23:38:24.349 ---
  Skipping n/a script '/root/.duply/MyProfile/pre'.
  --- Finished state OK at 23:38:24.400 - Runtime 00:00:00.051 ---

  --- Start running command BKP at 23:38:24.447 ---
  LFTP version is 4.3.6
  Reading globbing filelist /root/.duply/MyProfile/exclude
  Local and Remote metadata are synchronized, no sync needed.
  Traceback (most recent call last):
    File "/usr/local/bin/duplicity", line 1532, in <module>
    File "/usr/local/bin/duplicity", line 1526, in with_tempdir
    File "/usr/local/bin/duplicity", line 1380, in main
    File "/usr/local/bin/duplicity", line 1405, in do_backup
    File "/usr/local/lib/python2.7/dist-packages/duplicity/collections.py", 
line 710, in set_values
      self.get_backup_chains(partials + backend_filename_list)
    File "/usr/local/lib/python2.7/dist-packages/duplicity/collections.py", 
line 835, in get_backup_chains
    File "/usr/local/lib/python2.7/dist-packages/duplicity/collections.py", 
line 829, in add_to_sets
      if new_set.add_filename(filename):
    File "/usr/local/lib/python2.7/dist-packages/duplicity/collections.py", 
line 101, in add_filename
    File "/usr/local/lib/python2.7/dist-packages/duplicity/collections.py", 
line 149, in set_manifest
    File "/usr/local/lib/python2.7/dist-packages/duplicity/collections.py", 
line 128, in set_files_changed
      mf = self.get_manifest()
    File "/usr/local/lib/python2.7/dist-packages/duplicity/collections.py", 
line 250, in get_manifest
      return self.get_local_manifest()
    File "/usr/local/lib/python2.7/dist-packages/duplicity/collections.py", 
line 225, in get_local_manifest
      return manifest.Manifest().from_string(manifest_buffer)
    File "/usr/local/lib/python2.7/dist-packages/duplicity/manifest.py", line 
207, in from_string
      assert filecount == len(self.files_changed)

  23:38:36.860 Task 'BKP' failed with exit code '30'.
  --- Finished state FAILED 'code 30' at 23:38:36.860 - Runtime 00:00:12.412 ---

  --- Start running command POST at 23:38:36.930 ---
  Skipping n/a script '/root/.duply/MyProfile/post'.
  --- Finished state OK at 23:38:36.983 - Runtime 00:00:00.052 ---

  Probably the version of python got updated in the meantime, but I'm
  not sure about this.

  Similar tickets, eventually this bug report is a duplicate of those:
  - https://bugs.launchpad.net/duplicity/+bug/1485579
  - https://bugzilla.redhat.com/show_bug.cgi?id=1288702

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