finder – How to remove a file which name seems to be “.” on an SMB share?

Overview

Incorrect specification of an argument in a commandline tool (details below) has led to the creation of a file literally named “.”. I have already found out that directly trying to delete in Finder will trigger deletion of all content in the containing folder (fortunately this is a temporary folder), but still not the “.” file itself. Moreover, no folders containing this file can be successfully deleted, neither with Finder nor from bash/zsh shell.

How can one actually delete (or rename) such a file?

Attempts to delete from zsh

For example:

mytmp % ls -hal
total 65
drwx------  1 user  staff    16K Aug 21 11:20 .
-rwx------  1 user  staff     0B Aug 21 09:51 .
drwx------  1 user  staff    16K Aug 16 16:30 ..

mytmp % ls -aB
.   .   ..

mytmp % rm -rf '.'                   
rm: "." and ".." may not be removed

mytmp % cd ..

scratch % rm -rf mytmp
rm: mytmp: Permission denied

scratch % sudo rm -rf mytmp
rm: mytmp: Permission denied

I’ve also tried variations without -r, since really it is the non-directory version that is to be deleted.

I additionally tried the suggestion of @bmike to use the inode. While we can identify the inode, the deletion does not appear to work:

scratch % ls -ila mytmp
total 65
8056451580272514705 drwx------  1 user  staff  16384 Aug 21 11:20 .
8652239633868421122 -rwx------  1 user  staff      0 Aug 21 09:51 .
                  2 drwx------  1 user  staff  16384 Aug 21 11:43 ..

scratch % find mytmp -inum 8652239633868421122 -delete

## no change
scratch % ls -ila mytmp
total 65
8056451580272514705 drwx------  1 user  staff  16384 Aug 21 11:20 .
8652239633868421122 -rwx------  1 user  staff      0 Aug 21 09:51 .
                  2 drwx------  1 user  staff  16384 Aug 21 11:43 ..

Is it really named “.”?

@nohillside proposed to delimit the listings with x and y to see if it really is named “.”. From bash:

bash-3.2$ for i in .*; do echo x${i}y; done
x.y
x.y
x..y

Appears so.

@fd0 suggested printing non-printing characters with cat -vet. From bash:

bash-3.2$ ls -1a | cat -vet
.$
.$
..$

Again, seems identically named.

@nohillside Suggested running a Python server from the directory and display its directory listing:

Additional Background

The folder is on a network Volume, format SMB (OS X).

The tool that resulted in this was haplogrep, a Java-based CLI. One can install it through Conda via

conda install -c conda-forge -c bioconda haplogrep

The subcommand used was haplogrep classify, which has the following options:

mytmp % haplogrep classify

mtDNA Haplogroup Classifiction v2.4.0
https://github.com/seppinho/haplogrep-cmd
(c) Sebastian Schönherr, Hansi Weissensteiner, Lukas Forer, Dominic Pacher
[email protected]

[classify]
Missing required options: '--input=<in>', '--output=<out>', '--format=<format>'
Usage: haplogrep classify [--chip] [--extend-report] [--rsrs]
                          [--skip-alignment-rules] [--write-fasta]
                          [--write-fasta-msa] --format=<format>
                          [--hetLevel=<hetLevel>] [--hits=<hits>] --in=<in>
                          [--lineage=<lineage>] [--metric=<metric>] --out=<out>
                          [--phylotree=<tree>]
      --chip                VCF data from a genotype chip
                              Default: false
      --extend-report       Add flag for a extended final output
                              Default: false
      --format=<format>     Specify input file format: vcf, fasta or hsd
      --hetLevel=<hetLevel> Add heteroplasmies with a level > X from the VCF
                              file to the profile (default: 0.9)
      --hits=<hits>         Calculate best n hits
      --in, --input=<in>    Input VCF, fasta or hsd file
      --lineage=<lineage>   Export lineage information as dot file, \n0=no
                              tree, 1=with SNPs, 2=only structure, no SNPs
      --metric=<metric>     Specifiy other metrics (hamming or jaccard) than
                              default (kulczynski)
      --out, --output=<out> Output file location
      --phylotree=<tree>    Specify phylotree version
      --rsrs                Use RSRS Version
                              Default: false
      --skip-alignment-rules
                            Skip mtDNA nomenclature fixes based on rules for
                              FASTA import
                              Default: false
      --write-fasta         Write results in fasta format
                              Default: false
      --write-fasta-msa     Write multiple sequence alignment (_MSA.fasta)
                              Default: false

I misinterpreted the “Output file location” description of the --out argument as asking for a path, leading me to use --out . and thus resulting in creating a file named “.”.

Renaming

The file itself cannot be renamed in Finder or with mv, however, the containing folder can be renamed.