Hi,

I am trying to align whole genome fastqs to bams using samtools, however my shell script crashes with the error:

CMD: /projects/ps-gleesonlab/gleeson-lab/bin/bwa mem -M -R @RG ID:E00378:139:HJC3CCCXX:2 LB:missing147984366 PL:illumina SM:CCH-3020-3-3 /projects/ps-gleesonlab/resources/hg38.fa /oasis/scratch/comet/rmande/temp_project/06_21_2016/CCH-3020-3-3_reprocess/missing147984366_E00378:139:HJC3CCCXX:2_se.fq.gz [main] Real time: 134290.564 sec; CPU: 135419.789 sec failed on merge read groups for library:missing147984366:/oasis/scratch/comet/rmande/temp_project/06_21_2016/CCH-3020-3-3_reprocess/missing147984366_WGS.bam doesn't exist

I have very little samtools experience so I'm not too sure what the problem is. Any advice would be appreciated,