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Oxford Nanopore's Basecaller
https://nanoporetech.com/
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Problem downloading model RNA #1024

Closed MarioRinBarr closed 1 month ago

MarioRinBarr commented 1 month ago

Hi, I am trying to use the new models for m5C and inosine_m6A modification RNA with dorado 0.8. When I use the command "dorado download" to download all the available models it downloads all the previous models, but it does not download any model for modified bases with v5.1.0. Also, using the command "dorado download --model rna004_130bps_hac@v5.1.0_m5C@v1" dorado simply does not download anything. Is there any problem with these models or is my computer? Thank you very much

HalfPhoton commented 1 month ago

Can you please attach the stderr output and the full commands used?

Salvobioinfo commented 1 month ago

Hello everyone, It seems like a common issue that I’ve also experienced. Even when I run “dorado downlaod --list,” the new models are not being displayed.

HalfPhoton commented 1 month ago

Can I please ask you to report the output from dorado --version and dorado download --list?

Salvobioinfo commented 1 month ago

Here the output:

dorado -v

[2024-09-18 17:10:27.424] [info] Running: “-v”

0.7.0+71cc744`

and

dorado download --list 
[2024-09-18 17:08:40.429] [info] Running: “download” “--list”
[2024-09-18 17:08:40.429] [info] > modification models
[2024-09-18 17:08:40.429] [info]  - dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1
[2024-09-18 17:08:40.430] [info]  - dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1
[2024-09-18 17:08:40.430] [info]  - dna_r9.4.1_e8_sup@v3.3_5mCG@v0.1
[2024-09-18 17:08:40.430] [info]  - dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0
[2024-09-18 17:08:40.430] [info]  - dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0
[2024-09-18 17:08:40.430] [info]  - dna_r9.4.1_e8_sup@v3.3_5mCG_5hmCG@v0
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_260bps_fast@v3.5.2_5mCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_260bps_hac@v3.5.2_5mCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_260bps_sup@v3.5.2_5mCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_400bps_fast@v3.5.2_5mCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_400bps_hac@v3.5.2_5mCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_400bps_sup@v3.5.2_5mCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_260bps_fast@v4.0.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_260bps_hac@v4.0.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_260bps_sup@v4.0.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_400bps_fast@v4.0.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_400bps_hac@v4.0.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.0.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.430] [info]  - dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_hac@v4.2.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v2
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v3.1
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC@v2
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v2
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v3
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC_5hmC@v1
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1
[2024-09-18 17:08:40.431] [info]  - dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v1
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v1
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v1
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v1
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v1
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v1
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v1
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v1
[2024-09-18 17:08:40.432] [info]  - dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1
[2024-09-18 17:08:40.432] [info]  - rna004_130bps_sup@v3.0.1_m6A_DRACH@v1
[2024-09-18 17:08:40.433] [info]  - rna004_130bps_hac@v5.0.0_m6A@v1
[2024-09-18 17:08:40.433] [info]  - rna004_130bps_sup@v5.0.0_m6A@v1
[2024-09-18 17:08:40.433] [info]  - rna004_130bps_hac@v5.0.0_pseU@v1
[2024-09-18 17:08:40.433] [info]  - rna004_130bps_sup@v5.0.0_pseU@v1
[2024-09-18 17:08:40.433] [info] > stereo models
[2024-09-18 17:08:40.433] [info]  - dna_r10.4.1_e8.2_4khz_stereo@v1.1
[2024-09-18 17:08:40.433] [info]  - dna_r10.4.1_e8.2_4khz_stereo@v1.1
[2024-09-18 17:08:40.433] [info]  - dna_r10.4.1_e8.2_5khz_stereo@v1.1
[2024-09-18 17:08:40.433] [info]  - dna_r10.4.1_e8.2_5khz_stereo@v1.2
[2024-09-18 17:08:40.433] [info]  - dna_r10.4.1_e8.2_5khz_stereo@v1.3
[2024-09-18 17:08:40.433] [info] > simplex models
[2024-09-18 17:08:40.433] [info]  - dna_r9.4.1_e8_fast@v3.4
[2024-09-18 17:08:40.433] [info]  - dna_r9.4.1_e8_hac@v3.3
[2024-09-18 17:08:40.433] [info]  - dna_r9.4.1_e8_sup@v3.3
[2024-09-18 17:08:40.433] [info]  - dna_r9.4.1_e8_sup@v3.6
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_260bps_fast@v3.5.2
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_260bps_hac@v3.5.2
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_260bps_sup@v3.5.2
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_fast@v3.5.2
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_hac@v3.5.2
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_sup@v3.5.2
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_260bps_fast@v4.0.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_260bps_hac@v4.0.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_260bps_sup@v4.0.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_fast@v4.0.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_hac@v4.0.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.0.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_260bps_fast@v4.1.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_260bps_hac@v4.1.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_260bps_sup@v4.1.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_fast@v4.1.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_hac@v4.1.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.1.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_fast@v4.2.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_hac@v4.2.0
[2024-09-18 17:08:40.434] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.2.0
[2024-09-18 17:08:40.435] [info]  - dna_r10.4.1_e8.2_400bps_fast@v4.3.0
[2024-09-18 17:08:40.435] [info]  - dna_r10.4.1_e8.2_400bps_hac@v4.3.0
[2024-09-18 17:08:40.435] [info]  - dna_r10.4.1_e8.2_400bps_sup@v4.3.0
[2024-09-18 17:08:40.435] [info]  - dna_r10.4.1_e8.2_400bps_fast@v5.0.0
[2024-09-18 17:08:40.435] [info]  - dna_r10.4.1_e8.2_400bps_hac@v5.0.0
[2024-09-18 17:08:40.435] [info]  - dna_r10.4.1_e8.2_400bps_sup@v5.0.0
[2024-09-18 17:08:40.435] [info]  - rna002_70bps_fast@v3
[2024-09-18 17:08:40.435] [info]  - rna002_70bps_hac@v3
[2024-09-18 17:08:40.435] [info]  - rna004_130bps_fast@v3.0.1
[2024-09-18 17:08:40.435] [info]  - rna004_130bps_hac@v3.0.1
[2024-09-18 17:08:40.435] [info]  - rna004_130bps_sup@v3.0.1
[2024-09-18 17:08:40.435] [info]  - rna004_130bps_fast@v5.0.0
[2024-09-18 17:08:40.435] [info]  - rna004_130bps_hac@v5.0.0
[2024-09-18 17:08:40.435] [info]  - rna004_130bps_sup@v5.0.0
HalfPhoton commented 1 month ago

@Salvobioinfo v5.1.0 models are only available in dorado 0.8.0

HalfPhoton commented 1 month ago

@MarioRinBarr, any updates on this issue?

shuyi122425 commented 1 month ago

@Salvobioinfo v5.1.0 models are only available in dorado 0.8.0 I encountered an issue where I attempted to manually download two models in dorado 0.8.0, "rna004_130bps_hac@v5.1.0" and "rna004_130bps_sup@v5.1.0". While I successfully downloaded the "hac" version, I encountered difficulties with the "sup" version. Could you please know why this occurred?