pod5-file-format

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Metadata editing in pod5 files

10

Hi, we were running into an error during dorado basecalling (of recovered files after a failed run) due to incorrect sequencing kit: [2023-12-15 14:35:04.358] [error] Unknown sequencing_kit: FLO-PRO114M So then...

DCossey

pod5 filter freeze

3

Hello, When running `pod5 filter` I often get a freeze for the process in a random manner. Rerunning it usually results in successful completion. It is annoying because it does...

diego-rt

Pod 5 subsets

1

Does this program allow one to search out reads of interest, organize them and then work again with them? For example, when i am interested in a subset of reads,...

Jeff-Field

Q: `pod5 subset <..> --threads` takes a lot of resources

2

I just started using `pod5 subset` to regroup my POD5 data per-channel to optimize `dorado duplex` basecalling speed. The default setting for `--threads` is 4, I was brave and set...

sklages

memory error

13

Hi there, Im using pod5 python API to load signals in to another file. But I meet this error when I iterate through the pod5 reader. ```bash File "/rshare1/ZETTAI_path_WA_slash_home_KARA/home/coalball/projects/myNanoporeProject/extract/extract.py", line...

aCoalBall

The readme stated that setting threads to less than 1 would make it use all threads. I just got an error that threads needs to be at least 1

cfblaeb

pod5 subset cannot shard a large aggregate pod5 file

6

Using python 3.7 and pod5 0.2.4. I'm trying to use pod5 subset to break up a large pod5 file into smaller ones, but it crashes with a strange error. I...

billytcl

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

1

Python 3.7, pod5 0.2.4 Using this command to catch exceptions on a SLURM HPC cluster: ``` pod5 convert fast5 --strict -f -o pod5/converted.pod5 -r -t 20 ./Seq_Output/ ``` It catches...

billytcl

pod5 don't seem to save much space on short reads

7

I have some fast5s of short reads (~170bp) that total 1.7T: ``` billylau@suzuki:/mnt/ix1/Seq_Runs/20230721_PRM_1377/Seq_Output$ find . -iname '*.fast5' -print0 | du -ch --files0-from=- | tail 20M ./20230721_1655_3E_PAQ68008_9290fd40/fast5_pass/barcode11/PAQ68008_pass_barcode11_9290fd40_633ff27b_61.fast5 20M ./20230721_1655_3E_PAQ68008_9290fd40/fast5_pass/barcode11/PAQ68008_pass_barcode11_9290fd40_633ff27b_35.fast5 19M ./20230721_1655_3E_PAQ68008_9290fd40/fast5_pass/barcode11/PAQ68008_pass_barcode11_9290fd40_633ff27b_14.fast5...

billytcl

More info on some read table values

13

Hey again, I wanted to know a little more about the following fields. ``` num_minknow_events, tracked_scaling_scale, tracked_scaling_shift, predicted_scaling_scale, predicted_scaling_shift, num_reads_since_mux_change, time_since_mux_change, ``` Specifically: `num_minknow_events` : What is this actually? is...

Psy-Fer