I aligned 108 FASTQ pairs with bwa-mem in one go, after alignment I transformed the SAMs into BAMs with samtools. I wrote the script so that I know when a pair starts and ends.
The job was completed, because I found 108 BAMs in the output directory and the script indicates that all pairs were processed.
I want to rule out the possibility that an error occured by searching for a message that could indicate that something went wrong. I am not asking for the exact message, but some string that is common and exclusive to all error messages, either for bwa-mem or samtools.
Thanks in advance