I am getting this error when running a test data set for Lyve-SET on RHEL 7. Is this an MPileup error or something else? This is the error that I am getting:

launch_varscan.pl: Creating a pileup /home/user/lyve-SET-1.1.4f/lambda/tmp/NC001416.fasta.wgsim.fastq.gz-reference.sorted.bam.mpileup
removed ‘/home/user/lyve-SET-1.1.4f/lambda/tmp/NC001416.fasta.wgsim.fastq.gz-reference.sorted.bam.1239.mpileup’
launch_varscan.pl: Running mpileup:
  echo "NC_001416.1
" | xargs -P 1 -n 1 -I {} sh -c 'echo "MPileup on {}" &gt;&amp;2; samtools mpileup -f lambda/reference/reference.fasta 
-Q 0 -B  --region "{}" /home/user/lyve-SET-1.1.4f/lambda/bam/NC001416.fasta.wgsim.fastq.gz-reference.sorted.bam &gt; 
/home/user/lyve-SET-1.1.4f/lambda/tmp/NC001416.fasta.wgsim.fastq.gz-reference.sorted.bam.$$.mpileup'
MPileup on NC_001416.1
mpileup: unrecognized option '--region'
open: No such file or directory
[mpileup] failed to open NC_001416.1: No such file or directory
launch_varscan.pl: main::mpileup: ERROR with xargs and samtools mpileup
Stopped at /home/arahat/lyve-SET-1.1.4f/scripts/launch_varscan.pl line 106.
QSUB ERROR
31488
launch_set.pl: Schedule::SGELK::command: ERROR with command: Inappropriate ioctl for device
  /usr/bin/perl /home/user/lyve-SET-1.1.4f/lambda/log/SGELK/qsub.2705.pl
Stopped at /home/user/lyve-SET-1.1.4f/scripts/../lib/Schedule/SGELK.pm line 661.
set_test.pl: ERROR: died while trying to run COMMAND
  launch_set.pl lambda --numcpus 1 --numnodes 20
set_test.pl: See if you have the correct software installed for this command.
6400 at /home/arahat/lyve-SET-1.1.4f/scripts/set_test.pl line 94.
make: *** [test] Error 25


I think the main problem is the "mpileup: unrecognized option --region", which seems to be blank. In the beginning of the block, it says creating pileup and then it immediately removes the file, probably to create the pipeline file.

I cannot change the code for Lyve-SET pipelining or create shell scripts for the pipeline because I am only configuring my server for use with the genome sequencing pipeline. Would this be a problem with the data set or some tool that I need to install? Any insight would be appreciated.
The samtools v0.1.19 manual confirms that there is no --region option.  In that version there is only the -r argument to pass in the targeted region.  If you update to a newer version of samtools this should execute correctly