there are not enough pairs message on screen when running BWA MEM

[M::mem_pestat] low and high boundaries for proper pairs: (150, 353)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::mem_process_seqs] Processed 99010 reads in 5.077 CPU sec, 4.721 real sec
[M::process] read 99010 sequences (10000010 bp)...
[M::process] read 99010 sequences (10000010 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 46755, 5, 4)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (236, 252, 266)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (176, 326)
[M::mem_pestat] mean and std.dev: (252.49, 25.15)
[M::mem_pestat] low and high boundaries for proper pairs: (146, 356)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 99010 reads in 5.145 CPU sec, 4.968 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 46811, 3, 2)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (71, 126, 140)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 278)
[M::mem_pestat] mean and std.dev: (113.80, 56.09)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 347)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (236, 252, 266)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (176, 326)
[M::mem_pestat] mean and std.dev: (252.50, 25.34)
[M::mem_pestat] low and high boundaries for proper pairs: (146, 356)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::mem_process_seqs] Processed 99010 reads in 5.736 CPU sec, 5.375 real sec
[M::process] read 78246 sequences (7902846 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 36852, 8, 2)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (236, 252, 266)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (176, 326)
[M::mem_pestat] mean and std.dev: (252.51, 25.14)
[M::mem_pestat] low and high boundaries for proper pairs: (146, 356)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 78246 reads in 3.975 CPU sec, 3.678 real sec
[main] Version: 0.7.15-r1140
[main] CMD: bwa mem -M -R @RG\tID:HWI-ST610\tLB:D0DELACXX\tPL:ILLUMINA\tPM:HISEQ2000\tSM:Pool22 ../Reference/MTB.fa M_tuberculosis__Pool22_X60_1048__L6_ACTTGA_L006_R1.fastq M_tuberculosis__Pool22_X60_1048__L6_ACTTGA_L006_R2.fastq
[main] Real time: 926.964 sec; CPU: 905.573 sec

All of my reads having this message while aligning that there are not enough pairs. However, I have checked it everything is fine in the files. I ran the following command:

bwa mem \
  -M \
  -R '@RG\tID:HWI-ST610\tLB:D0DELACXX\tPL:ILLUMINA\tPM:HISEQ2000\tSM:Pool22' \
  ../Reference/MTB.fa M_tuberculosis__Pool22_X60_1048__L6_ACTTGA_L006_R1.fastq \
  M_tuberculosis__Pool22_X60_1048__L6_ACTTGA_L006_R2.fastq >  Pool22_X60_1048__L6.sam

Following is the output of the sam generated:

HWI-ST610:135:D0DELACXX:6:1101:2078:1958        99      AL123456.3      636003  60      101M
HWI-ST610:135:D0DELACXX:6:1101:2078:1958        147     AL123456.3      636141  60      101M
HWI-ST610:135:D0DELACXX:6:1101:2723:1941        77      *       0       0       *       *
HWI-ST610:135:D0DELACXX:6:1101:2723:1941        141     *       0       0       *       *
HWI-ST610:135:D0DELACXX:6:1101:2962:1941        83      AL123456.3      3869093 60      101M
HWI-ST610:135:D0DELACXX:6:1101:2962:1941        163     AL123456.3      3868962 60      101M
HWI-ST610:135:D0DELACXX:6:1101:3858:1995        77      *       0       0       *       *
HWI-ST610:135:D0DELACXX:6:1101:3858:1995        141     *       0       0       *       *
HWI-ST610:135:D0DELACXX:6:1101:4561:1958        83      AL123456.3      705624  60      101M
HWI-ST610:135:D0DELACXX:6:1101:4561:1958        163     AL123456.3      705476  40      81M20S
HWI-ST610:135:D0DELACXX:6:1101:4968:1941        99      AL123456.3      2427899 60      101M
HWI-ST610:135:D0DELACXX:6:1101:4968:1941        147     AL123456.3      2427966 60      101M
HWI-ST610:135:D0DELACXX:6:1101:5737:1941        99      AL123456.3      1394131 60      101M
HWI-ST610:135:D0DELACXX:6:1101:5737:1941        147     AL123456.3      1394270 60      101M
HWI-ST610:135:D0DELACXX:6:1101:5603:1944        99      AL123456.3      6566    60      101M

Should I be worried? as I think sam output is fine?

alignment bwa

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