Running duplex still 0% for the last 12 hours

[Sekuwanda]

Issue Report

Please describe the issue: My progress bar for running duplex is still at 0% for the last 12 hours.

Please provide a clear and concise description of the issue you are seeing and the result you expect.

Steps to reproduce the issue:

Please list any steps to reproduce the issue.

Run environment:

• Dorado version: 0.6.1+79b5da50
• Dorado command: ./cmake-build/bin/dorado duplex sup /Users/katofrank/Documents/BonoboFlow/SGA-MOH-24-4-24/3end/20240424_1242_MC-111480_FAY32808_e5691891/pod5 --reference /Users/katofrank/Documents/BonoboFlow/HXB2.fasta -t 4 > calls.bam
• Operating system: Mac Os
• Hardware (CPUs, Memory, GPUs): 8 CPU, 64 GB RAM
• Source data type (e.g., pod5 or fast5 - please note we always recommend converting to pod5 for optimal basecalling performance): pod5
• Source data location (on device or networked drive - NFS, etc.): device
• Details about data (flow cell, kit, read lengths, number of reads, total dataset size in MB/GB/TB): R10, SQK-NBD114-24, 4500 base pairs, 2.21 M/ 115.43 GB)
• Dataset to reproduce, if applicable (small subset of data to share as a pod5 to reproduce the issue):

Logs

• Please provide output trace of dorado (run dorado with -v, or -vv on a small subset)

[tijyojwad]

Hi @Sekuwanda - are you using one of the recent Macs with M1/M2/M3 silicon?

To make sure basecalling is working, can you run the same command but with --max-reads 10? This should run basecalling on the first 10 reads of your dataset so we can verify if you're getting any outputs at all.

[Sekuwanda]

Hi @Sekuwanda - are you using one of the recent Macs with M1/M2/M3 silicon?

To make sure basecalling is working, can you run the same command but with --max-reads 10? This should run basecalling on the first 10 reads of your dataset so we can verify if you're getting any outputs at all.

Hi @tijyojwad , In the meantime, I have an output from the previous command in the call.bam file.

But the progress bar is still at 0%.

Let me try out that command. with --max-reads 10

[Sekuwanda]

Here are the specifiations of the macbook pro, 16 inch 2019

Processor: 2.4 GHz 8-Core Intel Core i9 Graphics: Intel UHD Graphics 630 1536 MB Memory: 64 GB 2667 MHz DDR4

[Sekuwanda]

The --max-reads 10 command was not recognize. "./cmake-build/bin/dorado duplex sup /Users/katofrank/Documents/BonoboFlow/SGA-MOH-24-4-24/3end/20240424_1242_MC-111480_FAY32808_e5691891/pod5 --reference /Users/katofrank/Documents/BonoboFlow/HXB2.fasta -t 4 --max-reads 10 > trial.bam [2024-05-09 08:58:06.853] [info] Running: "duplex" "sup" "/Users/katofrank/Documents/BonoboFlow/SGA-MOH-24-4-24/3end/20240424_1242_MC-111480_FAY32808_e5691891/pod5" "--reference" "/Users/katofrank/Documents/BonoboFlow/HXB2.fasta" "-t" "4" "--max-reads" "10" [2024-05-09 08:58:06.854] [error] Unknown argument: --max-reads"

[HalfPhoton]

--max-reads is not available in duplex.

Please use -l / --read-ids

You can get a short list of reads from your pod5 data using the pod5 api like this:

pod5 view -IH pod5/ | head -n 10 > 10.ids
dorado duplex model reads .... --read-ids 10.ids > calls_10.bam

Although it might just be quicker to basecall a single file if you have multiple input pod5s

[malton-ont]

It looks like you're trying to do sup duplex + alignment on an Intel mac - this will be very slow as Intel macs will run dorado entirely on the CPU.

[Sekuwanda]

It looks like you're trying to do sup duplex + alignment on an Intel mac - this will be very slow as Intel macs will run dorado entirely on the CPU.

@malton-ont Thnk you. I have repeated the run but it seems the dorado duplex does not support --no trim option for keeping the barcodes. Hope the barcodes appear in the base calls.

[malton-ont]

@Sekuwanda,

Duplex mode does not currently support barcoding, so no trimming will be performed.