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Overview
Incorrect specification of an argument in a commandline instrument (particulars beneath) has led to the creation of a file actually named “.”. I’ve already came upon that immediately attempting to delete in Finder will set off deletion of all content material within the containing folder (luckily it is a non permanent folder), however nonetheless not the “.” file itself. Furthermore, no folders containing this file could be efficiently deleted, neither with Finder nor from bash/zsh shell.
How can one truly delete (or rename) such a file?
Makes an attempt to delete from zsh
For instance:
mytmp % ls -hal
whole 65
drwx------ 1 consumer workers 16K Aug 21 11:20 .
-rwx------ 1 consumer workers 0B Aug 21 09:51 .
drwx------ 1 consumer workers 16K Aug 16 16:30 ..
mytmp % ls -aB
. . ..
mytmp % rm -rf '.'
rm: "." and ".." will not be eliminated
mytmp % cd ..
scratch % rm -rf mytmp
rm: mytmp: Permission denied
scratch % sudo rm -rf mytmp
rm: mytmp: Permission denied
I’ve additionally tried variations with out -r
, since actually it’s the non-directory model that’s to be deleted.
I moreover tried the suggestion of @bmike to use the inode. Whereas we are able to determine the inode, the deletion doesn’t seem to work:
scratch % ls -ila mytmp
whole 65
8056451580272514705 drwx------ 1 consumer workers 16384 Aug 21 11:20 .
8652239633868421122 -rwx------ 1 consumer workers 0 Aug 21 09:51 .
2 drwx------ 1 consumer workers 16384 Aug 21 11:43 ..
scratch % discover mytmp -inum 8652239633868421122 -delete
## no change
scratch % ls -ila mytmp
whole 65
8056451580272514705 drwx------ 1 consumer workers 16384 Aug 21 11:20 .
8652239633868421122 -rwx------ 1 consumer workers 0 Aug 21 09:51 .
2 drwx------ 1 consumer workers 16384 Aug 21 11:43 ..
Is it actually named “.”?
@nohillside proposed to delimit the listings with x
and y
to see if it actually is called “.”. From bash
:
bash-3.2$ for i in .*; do echo x${i}y; carried out
x.y
x.y
x..y
Seems so.
@fd0 advised printing non-printing characters with cat -vet
. From bash
:
bash-3.2$ ls -1a | cat -vet
.$
.$
..$
Once more, appears identically named.
@nohillside Prompt working a Python server from the listing and show its listing itemizing:
Extra Background
The folder is on a community Quantity, format SMB (OS X).
The instrument that resulted on this was haplogrep
, a Java-based CLI. One can set up it by Conda by way of
conda set up -c conda-forge -c bioconda haplogrep
The subcommand used was haplogrep classify
, which has the next choices:
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]
Lacking required choices: '--input=<in>', '--output=<out>', '--format=<format>'
Utilization: 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 knowledge from a genotype chip
Default: false
--extend-report Add flag for a prolonged remaining output
Default: false
--format=<format> Specify enter file format: vcf, fasta or hsd
--hetLevel=<hetLevel> Add heteroplasmies with a degree > X from the VCF
file to the profile (default: 0.9)
--hits=<hits> Calculate finest n hits
--in, --input=<in> Enter VCF, fasta or hsd file
--lineage=<lineage> Export lineage info as dot file, n0=no
tree, 1=with SNPs, 2=solely construction, no SNPs
--metric=<metric> Specifiy different metrics (hamming or jaccard) than
default (kulczynski)
--out, --output=<out> Output file location
--phylotree=<tree> Specify phylotree model
--rsrs Use RSRS Model
Default: false
--skip-alignment-rules
Skip mtDNA nomenclature fixes primarily based on guidelines for
FASTA import
Default: false
--write-fasta Write leads to fasta format
Default: false
--write-fasta-msa Write a number of sequence alignment (_MSA.fasta)
Default: false
I misinterpreted the “Output file location” description of the --out
argument as asking for a path, main me to make use of --out .
and thus leading to making a file named “.”.
Renaming
The file itself can’t be renamed in Finder or with mv
, nonetheless, the containing folder could be renamed.
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