Richard Harris

Results 239 comments of Richard Harris

pod5 convert fast5 does not gracefully exit after an error when using "strict"

Thanks for reporting this @billytcl , we'll take a look at improving the error handling of the converter

--max-reads on dorado duplex

Hi @lucacozzuto, We'll discuss this feature and get back to you. Best regards, Rich

Request for fastq.gz read ID format change

Hi @andyjslee - This sounds like you're using duplex basecalled reads which write the read_ids as `idA;idB` - is this correct? I'll discuss this issue internally and we'll get back...

Request for fastq.gz read ID format change

Hi @andyjslee, Apologies for the delayed reply, and thank you for your feature request. After reviewing this, we won’t be moving forward with this change. The current format is required...

Restrict fastq output of demux to only samples included in the sample sheet

Hi @MostafaYA, we'll look into this as a feature and get back to you.

Failed to get modification model

Hi @KunFang93, There is no 6mA mods model for the r9.4.1 condition which is what the information messages are trying to communicate. ``` Failed to get modification model Found 2...

Too few arguments for '--mm2-opts'

Can you share the bam header in the `--resume-from` `${ModDir}/PAQ17395_1_sup.pass.m6A_pseU_m5C_inosine.mod.pass.bam` file? Dorado stores the original command used here and the error may be there. Best regards, Rich

Too few arguments for '--mm2-opts'

Yes, @tramelliwe you've identified the issue. Thank you. @kir1to455m, we can see that the sam header (which dorado re-uses arguments from when using resume) `--mm2-opts -k 15 -w 10 --secondary=no`...

Too few arguments for '--mm2-opts'

This has been fixed

pod5 merge hangs indefinitely at 99-100%(the last 20 pod5 have not been merged)

Interesting. Is this running in a conda environment or python environment? We occasionally see issues when running in conda. Are you able to merge the remaining 20 files into the...