Struggling to assign read groups with AddOrReplaceReadgroups

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Cora Olpe

• October 01, 2023 15:29

Hi,

I've spent hours trying to get AddOrReplaceReadgroups to work but I keep getting the same error so I'm hoping to find help here.

I am using GATK4

I have a file called 

plate1_rg_fields.txt

which looks like this:

UZH-CO-v001_CGTCTAAT 1 lib1 ILLUMINA unit1 1

UZH-CO-v001_AGACTCGT 1 lib1 ILLUMINA unit1 1

UZH-CO-v001_GCACGTCA 1 lib1 ILLUMINA unit1 1

etc etc etc it's 384 lines for a 384 well plate and it's tab delimited

I then run:

cat plate1_rg_fields.txt | while read SAMPLE ID LB PL PU SM

do

        gatk AddOrReplaceReadGroups --INPUT "$SAMPLE".bam --OUTPUT "$SAMPLE".rg.bam --RGID "$ID" --RGLB "$LB" --RGPL "$PL" --RGPU "$PU" --RGSM "$SM"

done

 

The tool starts and I can see this in my log.out file

it starts like this:

Using GATK jar /data/colpe/conda/envs/gatk_env/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar

Running:

    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /data/colpe/conda/envs/gatk_env/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar AddOrReplaceReadGroups --INPUT UZH-CO-v001_AGACTCGT.bam --OUTPUT UZH-CO-v001_AGACTCGT.rg.bam --RGID 1 --RGLB lib1 --RGPL ILLUMINA --RGPU unit1 --RGSM 1

But then the error I get is:

', doesn't.of tags in a SAM header must adhere to the regular expression '^[ -~]+$',but the value provided for RGSM, '1

Tool returned:

1

I don't understand this, as I specified the nr 1 as my RGSM so that should adhere to the required regex, no? The odd thing is, when I try just one sample it works (ie the first line of my tab delimited file) but when I then run it with all samples I get this error and no files are written. 

I would really appreciate some help, thank you!

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• 

  Gökalp Çelik

  • October 01, 2023 16:22
  • Edited

  Hi Cora Olpe

  Since single sample runs work fine but in a loop you are getting this error this is most likely not a GATK problem but a GNU tool read issue. It is possible that the line ending char \n or \r\n are getting in the way of SM when it is read from the stream. Is it possible for you to add another character seperated by tab to each line after SM column and try again? Alternatively you may add a middle step to trim whitespaces or line ending characters at each line as cat reads the file. 

  I hope this works for you. 

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• 

  Cora Olpe

  • October 01, 2023 16:25

  Hi Gökalp Celik,

   

  thanks so much, the extra character with tab solved it!

   

  best wishes

  Cora

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