Running CCS: unsupported sequencing chemistry combination

[polarbe]

Hello,

I was trying to run CCS on .bam files fetched from SRA.

I've just run into the following error.

There was no error msg for the isoseq tutorial bam file (alz.1perc.subreads.bam)

As I searched, the bindingkit-sequencingkit-basecallerversion combination described in the error msg is not in the supported combination list in ChemistryTable.cpp file in pbbam v1.7.0 (https://github.com/PacificBiosciences/pbbam/blob/develop/src/ChemistryTable.cpp).

Was it deprecated for the latest version? Should I downgrade pbbam or specify configurations for CCS program?

Could you let me know the exact requirements to run the scripts?

Any help would be appreciated!

[SziKayLeung]

Hello @polarbe,

Thanks for using our datasets! Some of the fetal samples were generated using an older chemistry kit so I've had to downgrade the ppbam version to ccs 3.4.1. The command to run the ccs is then exactly the same: ccs .subreads.bam .ccs.bam --minPasses=1. For all the other samples with newer chemistry, ccs was generated with the newer version (ccs 5.0.0).

Were you planning on rerunning all the samples, or just a few - I can double check which of the SRA samples were generated with the old chemistry kit.

Best,
Szi Kay

P.S I am also happy to share the CCS files/already downstream files generated

[polarbe]

@SziKayLeung Thanks a lot for your quick reply!

As you explained, the pipeline works with AdultA (SRR12660779) bam file!
I'll separate the rest of samples by reading .bam header and run the downstream with proper version of programs.
Thank you for your advice.

Could you share the intermediate files before/after minimap2 alignment? I just want to check the processing I did is right.

Best,
polarbe

[SziKayLeung]

Hello Polarbe,

Apologies for the late reply. I hope the alignment worked.
You can download the results from cupcake collapse (after alignment) into https://zenodo.org/record/7611814#.Y-DzwnbP2Ul for reference.

Best,
Szi Kay

[MenglinC]

Hello,

I was trying to run CCS on .bam files fetched from SRA.

I've just run into the following error.

There was no error msg for the isoseq tutorial bam file (alz.1perc.subreads.bam)

As I searched, the bindingkit-sequencingkit-basecallerversion combination described in the error msg is not in the supported combination list in ChemistryTable.cpp file in pbbam v1.7.0 (https://github.com/PacificBiosciences/pbbam/blob/develop/src/ChemistryTable.cpp).

Was it deprecated for the latest version? Should I downgrade pbbam or specify configurations for CCS program?

Could you let me know the exact requirements to run the scripts?

Any help would be appreciated!

Hi,I am new here!Could you please tell me how to convert the .sra files to .bam in your pipeline?