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

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

Yes!!!

It worked. Thanks a lot.

Gwenael