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.
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
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?