gunzip error: File not in gzip format

Question

[bioinformatics.girl]

So I'm currently trying to unzip an .rds.gz file with the command:

gunzip filename.rds.gz

But keep receiving the error,

gzip: filename.rds.gz: not in gzip format

Any suggestions?

[Friederike]

Why do you believe that this file was gzipped to begin with? How did you acquire the file? Did you generate it yourself?

What happens when you start R and, once R has started, you type:

myfile <- readRDS("filename.rds.gz")

[bioinformatics.girl]

I acquired it from NCBI: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132355

[Tusharika]

And which file is it from the NCBI page?

[bioinformatics.girl]

"GSE132355_E10-P45_umap_data.rds.gz"

[bioinformatics.girl]

Same error. Already tried this.

[Basti]

Your file may not be in gzip format because it has simply been archived and not compressed. Please could you check the format of your file with file filename.rds.gz?

Answer 1

[PeterKW]

If you intend to read the file you could use R (or any other software) as suggested by Friederike. Otherwise, as the error suggests, the file is likely not compressed. You can check the format using

file filename.rds.gz

A quick google search lead me to this site which gives a good description (there are multiple others).

[bioinformatics.girl]

I'm looking to decompress and read the file; yes, I have already looked at other resources.

[lieven.sterck]

Please answer to the question(s) people have raised here (especially the file command one). Doing so will increase the content and decrease the time it takes to resolve this.

[PeterKW]

OK, have you tried to read the file in R?

Answer 2

[patrickdm]

Try download it again.

Here I get:

$ file GSE132355_E10-P45_umap_data.csv.gz 

GSE132355_E10-P45_umap_data.csv.gz: gzip compressed data, was "GSE132355_E10-P45_umap_data.csv", last modified: Fri May 31 18:29:05 2019, from Unix, original size modulo 2^32 10020866

$ gunzip GSE132355_E10-P45_umap_data.csv.gz 

$ ls GSE132355_E10-P45_umap_data.csv

GSE132355_E10-P45_umap_data.csv

$ file GSE132355_E10-P45_umap_data.csv  GSE132355_E10-P45_umap_data.csv: CSV text

$ head GSE132355_E10-P45_umap_data.csv  ,X,Y,Z,Age,Cluster E10_AAACCTGAGAGAACAG,2.339453139,-1.460134786,-3.280235386,E10,Neuroepithelium E10_AAACCTGAGGGTTCCC,0.377776651,5.207414433,-13.76702484,E10,Endothelial cells E10_AAACCTGAGTGCTGCC,4.908790257,-2.062134981,-4.072996184,E10,Neuroepithelium E10_AAACCTGCAGCCACCA,2.984554671,-1.315386607,-4.15868427,E10,Neuroepithelium E10_AAACCTGCATTCCTGC,4.401765532,-1.712143088,-4.252494383,E10,Neuroepithelium E10_AAACCTGGTAGCGTAG,3.11400317,-1.501352402,-3.459717893,E10,Neuroepithelium E10_AAACCTGGTCAATGTC,3.4002515,-2.33864262,-4.068272767,E10,Meningeal cells E10_AAACCTGGTCTCCATC,3.289397802,-1.406725979,-3.971118807,E10,Neuroepithelium E10_AAACCTGGTCTGCAAT,3.285394114,-2.492063981,-4.035709575,E10,Meningeal cells

[lieven.sterck]

OP seems to have the .rds.gz file ?

[patrickdm]

whoops.... :s

$ file GSE132355_E10-P45_umap_data.rds.gz  
GSE132355_E10-P45_umap_data.rds.gz: gzip compressed data, was "GSE132355_E10-P45_umap_data.rds", last modified: Fri May 31 18:29:06 2019, from Unix, original size modulo 2^32 2797009

$ gunzip GSE132355_E10-P45_umap_data.rds.gz  

$ ls GSE132355_E10-P45_umap_data.rds 
GSE132355_E10-P45_umap_data.rds

$ file GSE132355_E10-P45_umap_data.rds 
GSE132355_E10-P45_umap_data.rds: gzip compressed data, from HPFS filesystem (OS/2, NT), original size modulo 2^32 4502300

Answer 3

[Gordon Smyth]

I had no trouble unzipping the file (gzip -d and 7-Zip Windows app both worked) and the unzipped file is valid RDS format:

> x <- readRDS("GSE132355_E10-P45_umap_data.rds")
> head(x)
          X         Y          Z Age
1 2.3394531 -1.460135  -3.280235 E10
2 0.3777767  5.207414 -13.767025 E10
3 4.9087903 -2.062135  -4.072996 E10
4 2.9845547 -1.315387  -4.158684 E10
5 4.4017655 -1.712143  -4.252494 E10
6 3.1140032 -1.501352  -3.459718 E10

[ATpoint]

Agree, works for me as well, so your download might be corrupted.