Duplex basecalling is impractically slow

[hasindu2008]

The command I ran is: dorado duplex dna_r10.4.1_e8.2_400bps_sup@v4.0.0 reads/ --pairs pairs_from_bam_hg2/pair_ids_filtered.txt
Now 19 hours, but only 120,000 reads are done, on 4xTesla V100. For 1.2M pairs, it will be a few days. GPUs are consistently running at 80-95% utilisation in nvidia-smi. Is it normal to be this slow?

[vellamike]

Hi, it’s possible that this is caused by a low pairing rate. Dorado v0.2.1 introduces performance improvements to Dupelx, could you try this?

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On Wed, 15 Feb 2023 at 23:36, Hasindu Gamaarachchi ***@***.***> wrote: The command I ran is: dorado duplex ***@***.*** reads/ --pairs pairs_from_bam_hg2/pair_ids_filtered.txt Now 19 hours, but only 120,000 reads are done, on 4xTesla V100. For 1.2M pairs, it will be a few days. GPUs are consistently running at 80-95% utilisation in nvidia-smi. Is it normal to be this slow? — Reply to this email directly, view it on GitHub <#98>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALYB7IYK7P57GYRCDECFDLWXVR63ANCNFSM6AAAAAAU5O6T7M> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[hasindu2008]

Keeps getting this with the newest dorado

 /install/dorado-0.2.1/bin/dorado duplex /install/dorado-0.2.1/models/dna_r10.4.1_e8.2_400bps_sup@v4.1.0  reads/  --pairs pairs_from_bam_hg2/pair_ids_filtered.txt > sup_duplex_hg2_pod.sam
[2023-02-17 14:32:33.612] [info] > Loading pairs file
[2023-02-17 14:32:35.223] [info] > Pairs file loaded
[2023-02-17 14:33:00.545] [info] > Reads basecalled: 0
[2023-02-17 14:33:00.545] [info] > Bases/s: 0.000000e+00
[2023-02-17 14:33:01.040] [error] toml::parse: file open error -> /install/dorado-0.2.1/models/dna_r10.4.1_e8.2_4khz_stereo@v1.1/config.toml

[vellamike]

Hi @hasindu2008 , is the model dna_r10.4.1_e8.2_4khz_stereo@v1.1 in the directory /install/dorado-0.2.1/models ? It is necessary to download this model with dorado download --model all

[hasindu2008]

Now the time for duplex is good with 0.2.1! Took only around 6 hours.

[vellamike]

That's great! We are working on further performance improvements so expect that 6 hours to go down further.