featureCounts Error: SAM_pairer_osr_next_name: Assertion `rlen < 1024' failed

[nachocab]

I get this error when I run featureCounts on an output file generated by STAR as BAM SortedByCoordinate:

|| Process BAM file xxx... ||
|| Paired-end reads are included. ||
|| Assign fragments (read pairs) to features... ||
featureCounts: input-files.c:3377: SAM_pairer_osr_next_name: Assertion `rlen < 1024' failed.
Aborted

Interestingly, if I run STAR again and I choose BAM Unsorted as the output parameters, featureCounts does not fail. Out of 20 samples that I'm analyzing only one gave me this error. What I would like to know is what the error means (in the code I see that rlen is the buffer for fread(), but I don't understand what would make it be more than 1024 bytes), and if I there is an easy way to identify what's causing it.

Thanks

[shi]

Hi @nachocab,

Could you send us your bam file offline so that we can figure out what caused the problem? Could you show us your command as well?

Wei

[nachocab]

Hi Shi,
Sure, no problem. How and where do I send it? It's 2.1GB

[shi]

Could you send it via CloudStor?

https://cloudstor.aarnet.edu.au/

[nachocab]

Hmm, I don't think so. I don't belong to any of those universities

[shi]

Sure. Maybe via dropbox? Or you can put it somewhere on internet and then we can download it.