Error in `[[.H5File`(f5_obj, basecaller_path)

[sunsetyerin]

Hi @adnaniazi, I got the error below and cannot interpret what is the problem. Can you please let me know what can I do to run tailfindr? Thanks in advance.

Warning message: package ‘tailfindr’ was built under R version 4.1.2 Error in[[.H5File(f5_obj, basecaller_path) : An object with name /read_00181928-5546-4115-9249-d9da44b2d809/Analyses/Basecall_1D_001 does not exist in this group Calls: find_tails ... explore_basecaller_and_fast5type -> [[ -> [[.H5File Execution halted Not cleaning up /path/path/.snakemake/scripts/tmpsym8ipb5.tailfindr.R

[adnaniazi]

Hi, Can you send me the tailfindr command that you are using?

[sunsetyerin]

Hi, Adnan, Thanks for your reply. I ran trailfindr command in snakemake environment. Wonder what is causing the problem. [image: Screen Shot 2022-07-04 at 11.43.21 AM.png]

On Mon, Jul 4, 2022 at 11:40 AM Adnan Niazi @.***> wrote:

Hi, Can you send me the tailfindr command that you are using?

— Reply to this email directly, view it on GitHub https://github.com/adnaniazi/tailfindr/issues/31#issuecomment-1174070052, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOF5765JITLBKGJ2MJUJPBTVSMVX7ANCNFSM52T2Q2PQ . You are receiving this because you authored the thread.Message ID: @.***>

[adnaniazi]

It seems like the snakemake command that is running tailfindr is telling tailfindr to use Basecall_1D_001 group which does not exist in your particular FAST5 files. You need to edit your snakemake command such that it uses Basecall_1D_000 group.

[adnaniazi]

Just read the snakemake pipeline code and change Basecall_1D_001 to Basecall_1D_000

[sunsetyerin]

Thanks, I will try that and let you know if it works okay.