HTseq error and 0kb output file

Question

[aimanbarki]

Hello, I am trying to run htseq and it ran and in the end generate the empty file. and slurm file show the following warning :

100000 GFF lines processed.
200000 GFF lines processed.
300000 GFF lines processed.
400000 GFF lines processed.
500000 GFF lines processed.
..
.
.
.
.
46600000 SAM alignment record pairs processed.
46700000 SAM alignment record pairs processed.
46800000 SAM alignment record pairs processed.
46900000 SAM alignment record pairs processed.
Warning: Mate records missing for 2 records; first such record: <SAM_Alignment object: Paired-end read 'A01877:57:HG32MDRX2:2:1135:7193:4398' aligned to chr4:[156414311,156414462)/->.
46973143 SAM alignment pairs processed.

[Marco Pannone]

Did you sort your reads by position? If so, try to sort them by name instead since it might be due to a bug in HTSeq. You might want to have a look at this post.