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?