Question: failed on merge read groups for library
0
gravatar for rmande
2.7 years ago by
rmande0
rmande0 wrote:

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,

alignment next-gen genome • 606 views
ADD COMMENTlink written 2.7 years ago by rmande0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2386 users visited in the last hour