Question: GZIP ERROR:-2 using featureCounts (Subread)
gravatar for gbreard
5 months ago by
gbreard10 wrote:


I am running STAR analysis of RNAseq samples on a Mac Terminal and I can go through the mapping and .bam file generation but when I launch my command featureCounts, I get in jam with a message "GZIP ERROR:-2" scrolling down and I can't stop the process with usual "Ctrl + C" . It seems to be a problem related to zip initial format but I am a bit lost (I begin). 

What is weird is that I could run it with previous samples using the same command. 

Here below is the command I typed: 

"featureCounts -T 4 -g GeneID -F 'SAF' -s 1 -M -O -a GB_SAF_20180531.txt -o Sample1_featureCounts.out Sample1_Aligned.sortedByCoord.out.bam & Sample1_counts.log "

Does anybody have an idea how to solve the problem?

Thank you in advance



rnaseq software error • 210 views
ADD COMMENTlink modified 4 months ago • written 5 months ago by gbreard10

Subread version number?

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ADD REPLYlink modified 5 months ago • written 5 months ago by Gordon Smyth37k
Answer: C: GZIP ERROR:-2 using featureCounts (Subread)
gravatar for Yang Liao
5 months ago by
Yang Liao100
Yang Liao100 wrote:

Hi Gwenael,

The "GZIP ERROR:-2" message sounds like an old bug in featureCounts. Which version of featureCounts did you use? If it was not the latest version (v1.6.3), you can try our latest version, which is available on

since this bug had been fixed in v1.6.3 of featureCounts.



ADD COMMENTlink written 5 months ago by Yang Liao100
Answer: GZIP ERROR:-2 using featureCounts (Subread)
gravatar for gbreard
4 months ago by
gbreard10 wrote:


It worked. Thanks a lot.


ADD COMMENTlink written 4 months ago by gbreard10
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