If you run this program, "module load samtools" should be pointed out the version of samtools because the default version is 1.2. Any version of great than 1.0 will cause an error like this: Samtools-htslib-API: bam_get_library() not yet implemented
/bin/bash: line 1: 15282 Aborted (core dumped) samtools rmdup "${OUTDIR}/sorted/${SAMPLENAME}${YMD}_sorted.bam" "${OUTDIR}/deduped/${SAMPLENAME}${YMD}_deduped.bam".
So here I recommended to load the samtools <1.0.
If you run this program, "module load samtools" should be pointed out the version of samtools because the default version is 1.2. Any version of great than 1.0 will cause an error like this: Samtools-htslib-API: bam_get_library() not yet implemented /bin/bash: line 1: 15282 Aborted (core dumped) samtools rmdup "${OUTDIR}/sorted/${SAMPLENAME}${YMD}_sorted.bam" "${OUTDIR}/deduped/${SAMPLENAME}${YMD}_deduped.bam". So here I recommended to load the samtools <1.0.