Question: GZIP ERROR:-2 using featureCounts (Subread)
0
gravatar for gbreard
7 months ago by
gbreard10
gbreard10 wrote:

Hello, 

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

Gwenael

 

rnaseq software error • 285 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by gbreard10

Subread version number?

You might also interested in: https://www.biorxiv.org/content/early/2018/07/26/377762

ADD REPLYlink modified 7 months ago • written 7 months ago by Gordon Smyth37k
Answer: C: GZIP ERROR:-2 using featureCounts (Subread)
2
gravatar for Yang Liao
7 months ago by
Yang Liao110
Australia
Yang Liao110 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 

 https://sourceforge.net/projects/subread/files/subread-1.6.3/

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

Cheers,

Yang

ADD COMMENTlink written 7 months ago by Yang Liao110
Answer: GZIP ERROR:-2 using featureCounts (Subread)
1
gravatar for gbreard
7 months ago by
gbreard10
gbreard10 wrote:

Yes!!!

It worked. Thanks a lot.

Gwenael

ADD COMMENTlink written 7 months ago by gbreard10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 190 users visited in the last hour