Error with bam files that has paired end reads + singletons

[bioinfo17]

Hi,

I used merged genome + transcriptome file with Hisat2 to retrieve all reads in my samples, and then converted the bam files to R1. fastq, R2.fastq + singletons files. I then used Hisat2 with the three files and used the transcriptome fasta file to pull out reads which is now in bam format to be used in Salmon. When I tried using Salmon using the transcriptome fasta file and the bam file, I get this error:

WARNING: Detected suspicious pair --- The proper-pair statuses are inconsistent: read1 [HWI-7001326F:36:C7J2GANXX:5:1104:13209:80405] : proper-pair; mapped; matemapped

read2 : [HWI-7001326F:36:C7J2GANXX:5:1104:13209:80405] : no proper-pair; mapped; matemapped

[2017-07-07 10:46:02.309] [jointLog] [warning]

ERROR: Found unpaired read in a paired-end library. The read was marked as unpaired in sequencing (not just unmapped).The two ends of a paired-end read should be adjacent. Don't know how to proceed; exiting!

I tried to sort the bam files using samtools sort -n but still I get the above error. Any advice please? Thanks