BWA error: no ID within the read group line

Question

[whb]

Hi,

I am trying to use parallel and bwa men to align fastqs in batch but it kept giving me the same error [E::bwa_set_rg] no ID within the read group line . I have tried different combination e.g. ' ' instead of " " or no quotes but none of them worked.

My fastq files names are:

153_D1_S9_R1_001.1607214816484_Cut_0.fastq.gz 
153_D1_S9_R3_001.1607214816484_Cut_0.fastq.gz 
153_ND1_S11_R1_001.1607216304845_Cut_0.fastq.gz 
153_ND1_S11_R3_001.1607216304845_Cut_0.fastq.gz

I have two text files TrimmedMeta.txt and TrimIDs.txt that contain the sample names and ID respectively as below:

TrimmedMeta.txt:

153_D1_S9
153_ND1_S11

TrimIDs.txt

1607214816484 
1607216304845

Code in bash script bwa_align.sh:

outdrive=/SAMs/
ref=/ref/GRCm39/GCF_000001635.27_GRCm39_genomic.fna
TAG="@RG\tID:{1}\tSM:{1}\tLB:{1}"

parallel --link -a TrimmedMeta.txt -a TrimIDs.txt bwa mem -R ${TAG} ${ref} {1}_R1_001.{2}_Cut_0.fastq.gz {1}_R3_001.{2}_Cut_0.fastq.gz '>'${outdrive}/{1}_output.sam

Did a --dry-run gave me what I expected:

bwa mem -R @RG\tID:153_D1_S9\tSM:153_D1_S9\tLB:153_D1_S9 ref/GRCm39/GCF_000001635.27_GRCm39_genomic.fna 153_D1_S9_R1_001.1607214816484_Cut_0.fastq.gz 153_D1_S9_R3_001.1607214816484_Cut_0.fastq.gz > /SAMs/153_D1_S9_output.sam
bwa mem -R @RG\tID:153_ND1_S11\tSM:153_ND1_S11\tLB:153_ND1_S11 ref/GRCm39/GCF_000001635.27_GRCm39_genomic.fna 153_ND1_S11_R1_001.1607216304845_Cut_0.fastq.gz 153_ND1_S11_R3_001.1607216304845_Cut_0.fastq.gz >/SAMs/153_ND1_S11_output.sam

However, when I submit the script gave me the error [E::bwa_set_rg] no ID within the read group line

What is the problem? Thanks

[Ram]

Can you try quoting the @RG.... argument passed to bwa mem?

[whb]

thanks for the reply. I thought the I have quoted it when I assign TAG variable. should I do "${TAG}"?

parallel --link -a TrimmedMeta.txt -a TrimIDs.txt bwa mem -R "${TAG}" ${ref} {1}_R1_001.{2}_Cut_0.fastq.gz {1}_R3_001.{2}_Cut_0.fastq.gz '>'${outdrive}/{1}_output.sam

[Ram]

Yeah, I'd quote the shell variable as well.

[whb]

I have tried the following but if gave me the same error:

parallel --jobs -1 --link -a TtrimmedMeta.txt -a TtrimIDs.txt bwa mem -R "@RG\tID:{1}\tSM:{1}\tLB:{1}" ${ref} {1}_R1_001.{2}_Cut_0.fastq.gz {1}_R3_001.{2}_Cut_0.fastq.gz '>'${outdrive}/{1}_output.sam

[chenyangkang24]

I met the same error when send this to PBS. I think something's going wrong with the quote, or @, or some special letter that PBS cannot recognize.

[whb]

Hi @chenyangkang24 I keep trying different combinations and this seems to work for me: "@RG'\'tID:{1}'\'tSM:{1}'\'tLB:{1}" instead of "@RG\tID:{1}\tSM:{1}\tLB:{1}" i.e. ticks around \ . Hope this helps!

[chenyangkang24]

Well that didn't work for me. I think we face different issue. In your case, maybe you can try '@RG\tID:{1}\tSM:{1}\tLB:{1}' as well?

[2380461260]

Hi, I met the same error when send this to PBS. Have you solved the problem? How did it work?

[seri]

Hi, I replaced \t with \\t and it worked. Hope this would be helpful.

[mgdrnl]

Thanks! This worked for me, something like this: TAG="@RG\\tID:${id}\\tSM:${id}\\tLB:${id}\\tPL:ILLUMINA"

[chenyangkang24]

Thank you anyway for the suggest

[whb]

Yes I did try '@RG\tID:{1}\tSM:{1}\tLB:{1}'. Did not work. Did you put "${TAG}"as well as TAG= "@RG'\'tID:{1}'\'tSM:{1}'\'tLB:{1}" or just ${TAG}? only "${TAG}" worked for me. But if it doesn't... I am not sure sorry.