[[!comment format=mdwn
 username="Ilya_Shlyakhter"
 avatar="http://cdn.libravatar.org/avatar/1647044369aa7747829c38b9dcc84df0"
 subject="another instance of git-annex-sync not being idempotent"
 date="2019-08-20T17:08:45Z"
 content="""
Here it is again:

[[!format sh \"\"\"
# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log

(master_env_v152_py36) 13:01  [viral-ngs-benchmarks] $ git annex sync
On branch is-import-rabies200
Your branch is up to date with 'origin/is-import-rabies200'.


It took 6.38 seconds to enumerate untracked files. 'status -uno'
may speed it up, but you have to be careful not to forget to add
new files yourself (see 'git help status').
nothing to commit, working tree clean
commit ok
remote: Enumerating objects: 2, done.
remote: Counting objects: 100% (2/2), done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 2 (delta 0), reused 1 (delta 0), pack-reused 0
Unpacking objects: 100% (2/2), done.
From github.com:broadinstitute/viral-ngs-benchmarks
   456ce673f18..c365f519845  is-import-rabies200        -> origin/is-import-rabies200
   456ce673f18..c365f519845  synced/is-import-rabies200 -> origin/synced/is-import-rabies200
Updating 456ce673f18..c365f519845
Fast-forward
 viral-ngs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
Already up to date.
pull origin ok
(master_env_v152_py36) 13:01  [viral-ngs-benchmarks] $ git annex sync
[is-import-rabies200 fe351a22089] git-annex in viral-ngs-benchmarks copy at /data/ilya-work/benchmarks/viral-ngs-benchmarks
 1 file changed, 1 insertion(+), 1 deletion(-)
commit ok
pull origin ok
Enumerating objects: 3, done.
Counting objects: 100% (3/3), done.
Delta compression using up to 8 threads
Compressing objects: 100% (2/2), done.
Writing objects: 100% (2/2), 959 bytes | 959.00 KiB/s, done.
Total 2 (delta 1), reused 0 (delta 0)
remote: Resolving deltas: 100% (1/1), completed with 1 local object.
To github.com:broadinstitute/viral-ngs-benchmarks.git
   c365f519845..fe351a22089  is-import-rabies200 -> synced/is-import-rabies200
push origin ok
(master_env_v152_py36) 13:02  [viral-ngs-benchmarks] $ git annex sync
On branch is-import-rabies200
Your branch is up to date with 'origin/is-import-rabies200'.


It took 6.40 seconds to enumerate untracked files. 'status -uno'
may speed it up, but you have to be careful not to forget to add
new files yourself (see 'git help status').
nothing to commit, working tree clean
commit ok
pull origin ok
(master_env_v152_py36) 13:04  [viral-ngs-benchmarks] $ uname -a
Linux ip-172-31-93-72.ec2.internal 4.14.133-113.112.amzn2.x86_64 #1 SMP Tue Jul 30 18:29:50 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
(master_env_v152_py36) 13:05  [viral-ngs-benchmarks] $ git annex version
git-annex version: 7.20190819-ge4cecf8
build flags: Assistant Webapp Pairing S3 WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
dependency versions: aws-0.21.1 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.1.0 ghc-8.6.5 http-client-0.5.14 persistent-sql\
ite-2.9.3 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_2\
24 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE\
2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2BP512E BLAKE2BP512 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224\
 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar git-lfs hook external
operating system: linux x86_64
supported repository versions: 5 7
upgrade supported from repository versions: 0 1 2 3 4 5 6
local repository version: 5

(master_env_v152_py36) 13:05  [viral-ngs-benchmarks] $ git remote -vv
dnanexus
from-ilya-work
from-ilya-work-01
from-ilya-work-02
from-ilya-work-03
ilya-work       /data/ilya-work (fetch)
ilya-work       /data/ilya-work (push)
my-ldir
mygs
origin  git@github.com:broadinstitute/viral-ngs-benchmarks.git (fetch)
origin  git@github.com:broadinstitute/viral-ngs-benchmarks.git (push)
s3-viral-ngs-benchmarks-web
viral-ngs-benchmarks-s3

(master_env_v152_py36) 13:06  [viral-ngs-benchmarks] $ git annex info --fast
repository mode: indirect
trusted repositories: 0
semitrusted repositories: 11
        00000000-0000-0000-0000-000000000001 -- web
        00000000-0000-0000-0000-000000000002 -- bittorrent
        0928dfcc-4dbe-4c24-a5a0-ac05c4a2c829 -- ilya-work
        0f104e0a-7126-4a4a-a342-e1bb049643f0 -- [from-ilya-work-03]
        1a276c39-67e3-4098-b469-747ab29fb97e -- viral-ngs-benchmarks copy on /ilya
        380286ac-2e8f-4285-94da-406eca323411 -- [dnanexus]
        40d047cf-3548-42d4-bdb6-e1e89a83b6df -- viral-ngs-benchmarks in broad laptop vm clone
        449efa47-a0e1-4376-a17f-42c7a1f509d1 -- Benchmarks for viral-ngs, stored on Amazon S3 [viral-ngs-benchmarks-s3]
        6b9993bb-df07-4409-be5e-05c1cd528165 -- [mygs]
        7205b5c0-4475-47c1-bfc1-39f57a487ac4 -- Website displaying benchmark summaries, stored on AWS S3 [s3-viral-ngs-benchmarks-web]
        b11d667d-2f3a-432a-a167-d90a1b0559cf -- viral-ngs-benchmarks copy at /data/ilya-work/benchmarks/viral-ngs-benchmarks [here]
untrusted repositories: 1
        b9f389c1-2a37-4200-96d9-0f07d97b5417 -- [my-ldir]
transfers in progress: none
available local disk space: 427.31 gigabytes (+10 gigabytes reserved)


# End of transcript or log.
\"\"\"]]


"""]]
