Pilon Error - Inappropriate call if not paired read

I was running Pilon to improve my genome assembly using pilon-1.16.jar. 

time nohup java -jar /data/software/pilon-1.16.jar --genome genome.fasta --frags SIPE1_filtered_sorted.bam --frags SIPE2_filtered_sorted.bam --frags SIPE3_filtered_sorted.bam --frags SIPE4_filtered_sorted.bam --frags SIPE5_filtered_sorted.bam --frags SIPE6_filtered_sorted.bam --jumps LIMP1_filtered_sorted.bam --jumps LIMP4c_filtered_sorted.bam --output Pilon_Output --changes --threads 22 --verbose &

Pilon version 1.16 Mon Dec 7 09:45:45 2015 -0500

Genome: genome.fasta
Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at com.simontuffs.onejar.Boot.run(Boot.java:340)
    at com.simontuffs.onejar.Boot.main(Boot.java:166)
Caused by: java.lang.IllegalStateException: Inappropriate call if not paired read
    at htsjdk.samtools.SAMRecord.requireReadPaired(SAMRecord.java:648)
    at htsjdk.samtools.SAMRecord.getProperPairFlag(SAMRecord.java:656)
    at org.broadinstitute.pilon.BamFile$$anonfun$scan$1.apply(BamFile.scala:273)
    at org.broadinstitute.pilon.BamFile$$anonfun$scan$1.apply(BamFile.scala:268)
    at scala.collection.Iterator$class.foreach(Iterator.scala:750)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1202)
    at org.broadinstitute.pilon.BamFile.scan(BamFile.scala:268)
    at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:92)
    at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$4.apply(GenomeFile.scala:92)
    at scala.collection.parallel.AugmentedIterableIterator$class.map2combiner(RemainsIterator.scala:115)
    at scala.collection.parallel.immutable.ParVector$ParVectorIterator.map2combiner(ParVector.scala:62)
    at scala.collection.parallel.ParIterableLike$Map.leaf(ParIterableLike.scala:1054)
    at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49)
    at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
    at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
    at scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51)
    at scala.collection.parallel.ParIterableLike$Map.tryLeaf(ParIterableLike.scala:1051)
    at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.internal(Tasks.scala:159)
    at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.internal(Tasks.scala:443)
    at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:149)
    at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443)
    at scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
    at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
    at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
    at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
    at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

Elsewhere I read files with reads mapped in different directions is causing the problem. So, I tried Pilon1.16 with only short insert libraries direction, it worked for a bit of time but eventually failed!

Since, I wanted to run pilon using both paired end and mate-pair libraries, I tried downloading the newest version of Pilonv1.18 which ALSO DID NOT SOLVE the above error.

Solution that worked for me:

So after exchannging few mails with the author, I finally extracted the reads whose pairs also mapped elsewhere in the genome and generated a BAM file. This time alone Pilon worked and still running without error! Let us see..if it will last! :)

I used the following command from the samtools.

samtools view -b -f 0x2 LIMP1.bam | samtools sort - LIMP1_mappedPairs_sorted.bam