To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Error details: SAM file doesn't have any read groups defined in the header. The GATK no longer supp

seyfimseyfim Member
edited July 2017 in Ask the GATK team

Hello I am new to GATK and I am attempting to follow the best practices for germline SNPs and Indels in Whole Exome sequencing. Here is my code:
import os, pprint

path = "/Users/seyfim/Directory/Marilyn/Eng_lamis Exom Hiseq Run 5-10-17/FASTQ Files/Eng_lamis-exome-38605575/CCF00239-01-001-46873888"
all=[ i for i in os.listdir(path) if i.endswith('.gz')]

for f in all:
print '\n\n\n\tsai making on ',f
os.system('bwa aln -t 32 -f '+f[:-9]+'.sai /Users/seyfim/Directory/Farshad/NEW_LIBRARY_FILES/hg19 '+f)
print '\n\n\tsai making has finished for ',f

all=[ i for i in os.listdir('.') if i.endswith('.sai')]

all.sort()
pprint.pprint(all)

while all:
first=all.pop(0)
second=all.pop(0)
name=first[5:-7]
print 'working on\n\n\t',first,'\n\t',second
os.system('bwa sampe -f '+name+'.sam -r "@RG\tID:0\tLB:'+name+'_LIB\tSM:'+name+'\tPL:ILLUMINA" /Users/seyfim/Directory/Farshad/NEW_LIBRARY_FILES/hg19 '+first+' '+second+' '+first[:-4]+'.fastq.gz '+second[:-4]+'.fastq.gz')
print 'Done working on ',name

If MeM:

path = "/Users/seyfim/Directory/Marilyn/Eng_lamis Exom Hiseq Run 5-10-17/FASTQ Files/Eng_lamis-exome-38605575/CCF00239-01-001-46873888"
all=[i for i in os.listdir(path) if i.endswith('gz')]
all.sort()
pprint.pprint(all)
while all:
fq1=all.pop(0)
fq2=all.pop(0)
f=fq1[:-9]
print 'working on\n\n\t',fq1,'\n\t',fq2,'\n\tAs ----> ',f
os.system('/Users/seyfim/software/bwa/bwa mem -M -t 24 -R "@RG\tID:bwa\tLB:'+f+'_LIB\tSM:'+f+'\tPL:ILLUMINA" /Users/seyfim/Directory/Farshad/NEW_LIBRARY_FILES/hg19.fa '+fq1+' '+fq2+' > '+f+'.sam')

I get this error:
Error details: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups

I thought I had taken care of this with
os.system('bwa sampe -f '+name+'.sam -r "@RG\tID:0\tLB:'+name+'_LIB\tSM:'+name+'\tPL:ILLUMINA"

Answers

Sign In or Register to comment.