Dear all, 

I am trying to use featurecounts for the first time. I am following exactly as mentioned in the Rsubread manual.

featureCounts(files='Aligned.nsortedByCoord.out.bam', annot='cuffcmp.combined.gtf', isGTFAnnotationFile=TRUE,isPairedEnd=TRUE)

after that the outcome looks like this

Processing Bcyt/Aligned.sortedByCoord.out.bam  ...

Warning: the feature on the 4366-th line has zero coordinate or zero lengths

Warning: the feature on the 26925-th line has zero coordinate or zero lengths

Warning: the feature on the 36138-th line has zero coordinate or zero lengths

Warning: the feature on the 38896-th line has zero coordinate or zero lengths

Warning: the feature on the 49896-th line has zero coordinate or zero lengths

Warning: the feature on the 51284-th line has zero coordinate or zero lengths

Warning: the feature on the 54658-th line has zero coordinate or zero lengths

Warning: the feature on the 55995-th line has zero coordinate or zero lengths

There are 84237 features loaded from the annotation file.
The 84237 features are sorted.
Number of chromosomes included in the annotation is 4940
The 0-th thread processed 0 reads
Number of fragments mapped to the features is: 0
Time cost = 1.6 seconds

It seems nothing is happening because there are zero processed reads. 

I am not sure what has went wrong? also please tell me more about the featurecount out come? how to read the file??

also what are the necessary things to look at while making BAM file? I am making my BAM file using STAR and it does not have unmapped reads. Also the GTF file that I am providing is either cuffcompare outcome or Scipio generated. I dont have GTF file available for my organism.

Thank you in advance.

Amol