I got this strange warning in the log of a recent gstacks run (reference aligned paired-end data):

Warning: Ignoring reads '4836788' and '4836788' that seem to belong to different samples ('SRR12010940' and 'SRR12011027').

I looked in the 2 bam files in question and each does contain a pair of reads with that ID, but they look pretty normal to me. I can't understand why gstacks would be confused about where they came from, since they are in different bam files.

SRR12010940:

4836788 73      2       511466  40      145M    =       511466  0       CATGATCACTTGATGGCAGTTGTGCGATTTGTTTCCCGGACTTGAAGTAATCCTGGGATCCGGGATTGTTTTTCCATATCCCGGGATTTCCTGGCATTTTAAAACTAGTGCGAAAAGGTCGAAACGTAACTGAAATGTACATTTT   JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ       AS:i:-18        XN:i:0  XM:i:3  XO:i:0  XG:i:0  NM:i:3  MD:Z:26T32T75A9 YT:Z:UP
4836788 133     2       511466  0       *       =       511466  0       AATTCCGCTCCTAAATGCTTATCTTTGACAGAAACGCGTATTTCGACTACCACTTGCAGTCTTCTTCAGTGTCAGTTACTCGTTTTTCAACTTCAACAGCAAACTGACAAACTTGAGCATATGTATTTTTGAAAGACTTAATACAAG FFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJFJFFJJJAJJJJJJJ     YT:Z:UP

SRR12011027:

4836788 99  2   511873  42  145M    =   511973  246 CATGCAACAGGTTACCACCTTTCCATTTCTACTGACGACATTGGCCGGAAAATCGTCAGGTGACTAAAGGTCTTGTTTGCTTCTTAGGTAAACTGTTTACGTTGTGTAGCCTCAGGAGAGTTTGTTTCTCTTCACAGAGAAGGAA   JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJJJJJJJJJJJJ   AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:145    YS:i:-3 YT:Z:CP
4836788 147 2   511973  42  146M    =   511873  -246    GTTTTGTAGCCTCAGGAGAGTTTGTTTCTCTTCACAGAGAAGGAAATAACGGATGATGCTTTGCGAAGCCAAGCTCTAACCGCAAGTAGGTTGGTATCATACCTGGACACGCCTGGACTGGCAGAAGTGTCAAAGATGTATAAATT  A<--JJJFJJJJJJJJJJJFAJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFF  AS:i:-3 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:3G142  YS:i:0  YT:Z:CP

Has anyone else ever seen a warning like this? Any ideas why it happened?