Here is the command I ran

abyss-pe \
  k=64 \
  name=5-1 \
  lib='lib1 lib2 lib3 lib4' \
  lib1='E21_S1_L001_R1_001.fastq E21_S1_L001_R2_001.fastq' \
  lib2='E21_S1_L002_R1_001.fastq E21_S1_L002_R1_001.fastq' \
  lib3='E21_S1_L003_R1_001.fastq E21_S1_L003_R2_001.fastq' \
  lib4='E21_S1_L004_R1_001.fastq E21_S1_L004_R2_001.fastq'

Here is the error I got:

abyss-map \
  -j2 \
  -l64 \
  E21_S1_L002_R1_001.fastq E21_S1_L002_R1_001.fastq 5-1-3.fa \
    | abyss-fixmate -l64 -h lib2-3.hist \
    | sort -snk3 -k4 \
    | DistanceEst -j2 -k64 -l64 -s200 -n10 -o lib2-3.dist lib2-3.hist
Building the suffix array...
Building the Burrows-Wheeler transform...
Building the character occurrence table...
error: duplicate read ID `NS500216:249:HF37WBGXX:2:11101:7210:1086/1'
error: `lib2-3.hist': No such file or directory
make: *** [lib2-3.dist] Error 1
make: *** Deleting file `lib2-3.dist'

I looked to see if there was really a duplicated read ID in the file for both sets of reads:

grep 'NS500216:249:HF37WBGXX:2:11101:7210' E21_S1_L002_R1_001.fastq
@NS500216:249:HF37WBGXX:2:11101:7210:1086 1:N:0:1
@NS500216:249:HF37WBGXX:2:11101:7210:6418 1:N:0:1

grep 'NS500216:249:HF37WBGXX:2:11101:7210' E21_S1_L002_R2_001.fastq
@NS500216:249:HF37WBGXX:2:11101:7210:1086 2:N:0:1
@NS500216:249:HF37WBGXX:2:11101:7210:6418 2:N:0:1

Anyone have any ideas of what to do now?