error running BWA

[honey]

I am running BWA using hg10 on paired end (100XPE) but I am getting error message- Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3

[bwa_aln_core] 168861678 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
SA-BWT inconsistency: seq_len is not the same. Abort!
line 20: 22365 Aborted
[samopen] SAM header is present: 84 sequences.
[sam_read1] reference 'ID:bwa PN:bwa VN:0.5.9-r16

27682

' is recognized as '*'.
[main_samview] truncated file.

What is wrong here and how can I fix it, It is happening with all the files.
Thanks