Question: How to parse text correctly for bowtie2 --rg parameter?
0
gravatar for MatthewP
6 months ago by
MatthewP880
China
MatthewP880 wrote:

I want to add --rg when runing bowtie2, but this will cause error:

$bowtie2 --un-conc-gz /Example/TestPipeline/Unmapped/BJBC001C --rg-id CL100137430L1 --rg SM:BJBC001C -x GRCh38 -1 /Example/CleanData/BJBC001C_R1.fq.gz -2 /Example/CleanData/BJBC001C_R2.fq.gz -S /Example/TestPipeline/Bam/BJBC001C.sam        
Use of uninitialized value $bt2_args[6] in join or string at /App/anaconda2/envs/DNA/bin/bowtie2 line 423.
Use of uninitialized value $bt2_args[7] in join or string at /App/anaconda2/envs/DNA/bin/bowtie2 line 423.
Use of uninitialized value in exists at /App/anaconda2/envs/DNA/bin/bowtie2 line 81.
Use of uninitialized value in exists at /App/anaconda2/envs/DNA/bin/bowtie2 line 81.
Use of uninitialized value $bt2_args[6] in join or string at /App/anaconda2/envs/DNA/bin/bowtie2 line 459.
Use of uninitialized value $bt2_args[7] in join or string at /App/anaconda2/envs/DNA/bin/bowtie2 line 459.

Either --rg SM:BJBC001C or --rg "SM:BJBC001C" causes the same error. Remove --rg parameter then no error, so I think this is the problem.

bowtie2 • 209 views
ADD COMMENTlink written 6 months ago by MatthewP880

What's the bowtie version you're using? Also, why is it $bowtie2 and not bowtie2?

ADD REPLYlink written 6 months ago by Ram32k

bowtie is v2.4.1
It's bowtie2 just I add \n before $ in my PS1 setting

ADD REPLYlink written 6 months ago by MatthewP880

OK, that part was a little confusing. I think it'd be better to exclude the shell prefix, especially if it's not obvious that it's a shell prefix.

It is indeed strange that you're seeing this. I don't see any reason why your command should fail. Are you using anaconda by the way? Isn't anaconda2 old?

ADD REPLYlink written 6 months ago by Ram32k

Not very old anaconda2. My version is 4.8.2, current(20200825) newest version is 4.8.4. I will try to reinstall bowtie2.

ADD REPLYlink written 6 months ago by MatthewP880

My point was to switch to anaconda3, not a newer version of anaconda2. Python2.7 is to be switched away from as much as possible.

ADD REPLYlink written 6 months ago by Ram32k
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