[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped

[tseemann]

When using -bam output.bam I get these warnings: What does this mean?

9400 paired-end reads have been processed in 0 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
81000 paired-end reads have been processed in 2 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
84400 paired-end reads have been processed in 2 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
103200 paired-end reads have been processed in 2 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
623800 paired-end reads have been processed in 17 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
765600 paired-end reads have been processed in 21 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
804600 paired-end reads have been processed in 22 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
999800 paired-end reads have been processed in 27 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
1119800 paired-end reads have been processed in 30 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
1522000 paired-end reads have been processed in 41 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
1647000 paired-end reads have been processed in 45 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
1910600 paired-end reads have been processed in 51 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
1966400 paired-end reads have been processed in 52 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
2095600 paired-end reads have been processed in 55 seconds...[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
All the 2505564 paired-end reads have been processed in 67 seconds.
     2360067 ( 94.19%) reads are mapped properly.
     2124292 ( 84.78%) reads are mapped in pairs.
        Estimated AvgCoverage = 97
        Duplication rate=98.34%
        Average read length = 151, Estimated fragment size = 313, insert size = 11

[zhaoxvwahaha]

@tseemann Hi tseemann, I encounter same warnings, do you have answer for this now?