Entering edit mode
8 months ago
therosng
•
0
Hi,
Trying to polish pbmm2 bam output from Pacbio long read data using gcpp.
>|> 20250117 17:56:42.183 -|- FATAL -|- Run -|- 0x793d21863180|| -|- gcpp ERROR: [pbbam] read group ERROR: basecaller version is too short:
gcpp version 2.0.2-2.0.2
The bam file header:
@RG ID:default PL:PACBIO DS:READTYPE=UNKNOWN PU:default SM:UnnamedSample PM:SEQUEL
I tried replacing the header with:
samtools addreplacerg -r '@RG\tID:134g1\tPL:PACBIO\tPU:m84066_240627_194840\tDS=GeneratedBy:Sequel-II;Version:10.1.0\tSM:ChickenSample' \
-o fixed.bam sorted.bam
My "fixed" bam header is now:
@PG ID:samtools.1 PN:samtools PP:samtools VN:1.13 CL:samtools addreplacerg -r @RG\tID:134g1\tPL:PACBIO\tPU:m84066_240627_194840\tDS:v10.1.0\tSM:ChickenSample -o fixed.bam sorted134g1broiler.bam
@RG ID:134g1 PL:PACBIO PU:m84066_240627_194840 DS:v10.1.0 SM:ChickenSample
But it's still giving me the same error. What is the correct header ID?
