ANS: Your gap.bed file, your haploid sequence file and/or your reference file are not consistent in format.
Make sure all the sequence ids in .bed, .fasta files are consistent (e.g.) all with "chr" or all without "chr". To correct the fasta file, you need to rename the chromosome id and reindex the fasta file.
Make sure the gap bed file doesn't contain gap information for extra chromosomes not found in fasta files. e.g. if you are spiking only into "chr22", remove any gaps defined for all other chromosomes.
ANS: This is a bug of wgsim, which is giving empty fq file even given non-empty but only a small number of generated reads. The way to avoid this is to increase your allele fraction or coverage.
ANS: To install pysam, you need to complie Samtools by default. Please fix samtools's dependencies first. For instance, uncurse_ may be missed in Linux system.
ANS: this is because of a bug of pybedtools 0.8.0 reported at: https://github.com/daler/pybedtools/issues/284.
use "pip2 install -U pybedtools==0.7.0" downgrade to avoid this bug for now.