Warning: Mate records missing HTSEQ

Question

[san96]

Hello everyone,

At the end of the quantification with HTSEQ I get this warning, why is it? is it a serious problem?

enrique@DE:~/analisis_maiz/quantificacion$ htseq-count -f bam ../alignements/SRR214880_sorted.bam -s no -i gene_id -r pos -t exon ../genome_anotacion/Zea_mays.Zm-B73-REFERENCE-NAM -5.0.55\ \(1\).gtf > SRR214880.txt

Final:

Warning: Mate records missing for 2 records; first such record: <SAM_Alignment object: Paired-end read 'SRR21488088.572155' aligned to 10:[80575814,80575871)/->. 5855076 alignment record pairs processed.

I sorted my bam files by coordinates and generated bam file indices.

[ATpoint]

Two records out of millions, so what? ;)