It seems that the issue with parallel git-annex-add is not yet quite fixed; I'm seeing it in the git-annex version 7.20190507-g0c2cc3d . Repeating the git-annex-add command succeeds in adding the files that failed the first time.

add benchmarks/rabies200/analysis-FK7BF7Q0761xKv6V3z3gzZgK/benchmark_variants/v1.23.0_spades-3.13.0-trinity-metaspades-01/inputs-local.json
git-annex: .git/annex/othertmp/inge11793-2931: rename: permission denied (Permission denied)
add benchmarks/rabies200/analysis-FK7BKGj0761VgPb22550gfBX/benchmark_variants/v1.23.0_spades-3.13.0-trinity-metaspades-01/inputs-local.json
git-annex: .git/annex/othertmp/inge11793-3330: rename: permission denied (Permission denied)
git-annex: add: 2 failed

Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)

git-annex has become an essential tool for organizing my bioinformatics data analyses. It scales well to large repos. It lets me keep track of analyses without locking myself into any specific cloud platform. It lets me quickly free up space on demand by moving data to cheaper storage, with the assurance that nothing will get lost. Thanks @joeyh for all your work on it.