sorting BAM file

Question

[Mohammad Amin]

I tried sorting the BAM file i created using gatk-package-4.2.5.0-local.jar SortSam the code is :

java -jar gatk-package-4.2.5.0-local.jar SortSam -I {path.bam} -O {path.sorted.bam}  -SO coordinate

but i encountered this error:

INFO: Failed to detect whether we are running on Google Compute Engine.
[Tue May 30 16:08:32 IRST 2023] Executing as hp@hp-HP-Pavilion-Laptop-15-cs3xxx on Linux 5.15.0-72-generic amd64; OpenJDK 64-Bit Server VM 11.0.19+7-post-Ubuntu-0ubuntu120.04.1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.2.5.0
[Tue May 30 16:08:32 IRST 2023] picard.sam.SortSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=314572800
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
htsjdk.samtools.SAMFormatException: Error parsing SAM header. @RG line missing SM tag. Line:
@RG ID:P1; File /media/hp/Amin_Ghalavand/NF2.cases/PGERA1905/p3.bam; Line number 95
    at htsjdk.samtools.SAMTextHeaderCodec.reportErrorParsingLine(SAMTextHeaderCodec.java:258)
    at htsjdk.samtools.SAMTextHeaderCodec.access$200(SAMTextHeaderCodec.java:46)
    at htsjdk.samtools.SAMTextHeaderCodec$ParsedHeaderLine.requireTag(SAMTextHeaderCodec.java:358)
    at htsjdk.samtools.SAMTextHeaderCodec.parseRGLine(SAMTextHeaderCodec.java:168)
    at htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:110)
    at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:704)
    at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:298)
    at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:176)
    at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:406)
    at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:209)
    at picard.sam.SortSam.doWork(SortSam.java:152)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
    at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)

what seems to be the problem?

[GenoMax]

Error parsing SAM header. @RG line missing SM tag.

Looks like you did not include SM tags when you added read groups.

[ATpoint]

You can simply use samtools sort to get rid of this read group nonsense these Broad institute tools always complain about.