Question: Undo a shell script when input file is overwritten
0
gravatar for rse
10 months ago by
rse90
Singapore
rse90 wrote:

Hi,

Is it possible to redo a shell script? I overwrote my files running a shell script

I ran nohup sh 1.sh
But my output file was same as the input file, so it overwrote my input file

Thank you

next-gen • 389 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by rse90

Changed the title to make it more specific, added the additional information provided in the comments to the original question, cleaned up comments, and moved comments to answer so you can mark them as accepted.

ADD REPLYlink written 10 months ago by WouterDeCoster43k

Thank you for your help. I don't have backup of file but i am still optimistic. I used zcat and gzip to merge and zip the files using : zcat file1.fastq.gz file2.fastq.gz | gzip -c > file1.fastq.gz

ADD REPLYlink written 10 months ago by rse90
2

You could just do cat file1.fastq.gz file2.fastq.gz > merged.fastq.gz. There is no need to zcat/gzip again.

ADD REPLYlink written 10 months ago by WouterDeCoster43k

zcat already concatanates compressed files, there is no need for gzip in this command:

zcat file1.fastq.gz file2.fastq.gz > file1.fastq.gz
ADD REPLYlink modified 10 months ago • written 10 months ago by ATpoint30k

Ok, thanks. But my file1.gz is empty now

ADD REPLYlink written 10 months ago by rse90

I found this link : https://superuser.com/questions/292728/critical-gzip-mistake-help-how-to-undo-gzip-r/1426042#1426042 Will gzip -r work? Thanks

ADD REPLYlink written 10 months ago by rse90

Sorry, did not pay attention. Use cat to concatenate:

cat file1.fastq.gz file2.fastq.gz > new.fastq.gz

Also do not write to a file with identical name as the input.

ADD REPLYlink modified 10 months ago • written 10 months ago by ATpoint30k
0
gravatar for Carambakaracho
10 months ago by
Carambakaracho2.0k
Germany/Cologne
Carambakaracho2.0k wrote:
  • restore input from backup
  • recompute input

there's not much else you can do... sooner or later, that happens to everybody

ADD COMMENTlink modified 10 months ago • written 10 months ago by Carambakaracho2.0k
2
rm * .bam
ADD REPLYlink written 10 months ago by ATpoint30k

Lol...don't want to delete more files

ADD REPLYlink written 10 months ago by rse90
0
gravatar for WouterDeCoster
10 months ago by
Belgium
WouterDeCoster43k wrote:

Your input file is gone. Unless you have a backup somewhere, there is no way to restore it or "redo" the script.

Pro tip: make sure your input files are read-only (chmod -w) to avoid loss of data.

ADD COMMENTlink modified 10 months ago • written 10 months ago by WouterDeCoster43k

You mean chmod -w, no?

ADD REPLYlink written 10 months ago by RamRS25k

Certainly! Will change my post.

ADD REPLYlink written 10 months ago by WouterDeCoster43k
0
gravatar for Joe
10 months ago by
Joe16k
United Kingdom
Joe16k wrote:

As others have said, your data is long gone, unless:

  • You have the original input data, and can simply recompute it easily enough.
  • Your server/SysAdmin has configured regular snapshots, but this isn't that common, and would probably only get you to whereever you were yesterday.

There's no such thing as a recycle bin on Unix, so when you delete stuff - you really delete stuff.

ADD COMMENTlink written 10 months ago by Joe16k
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