nanoporetech/dorado issues and pull requests

#100 - polyA sequence are not called by dorado

Issue - State: closed - Opened by yul96 over 1 year ago - 27 comments
Labels: enhancement

#99 - version and verbose have the same short-hand flag

Issue - State: closed - Opened by pwh124 over 1 year ago - 2 comments
Labels: bug

#98 - Duplex basecalling is impractically slow

Issue - State: closed - Opened by hasindu2008 over 1 year ago - 5 comments

#97 - std::runtime error due to shape mismatch

Issue - State: closed - Opened by ddubocan over 1 year ago - 3 comments
Labels: bug

#96 - Read splitting feature request

Issue - State: closed - Opened by Psy-Fer over 1 year ago - 2 comments
Labels: enhancement

#95 - Stereo mode on deep sequencing dataset

Issue - State: closed - Opened by asan-emirsaleh over 1 year ago - 3 comments
Labels: question

#94 - Duplex mode ignoring most of the reads (only ~800 output out of ~13,000)

Issue - State: closed - Opened by hasindu2008 over 1 year ago - 4 comments

#93 - R9 modified basecalling

Issue - State: closed - Opened by AlexanRNA over 1 year ago - 5 comments
Labels: bug

#92 - Forked master

Pull Request - State: closed - Opened by hasindu2008 over 1 year ago

#91 - Duplex basecalling using pair list - many pairs ignored?

Issue - State: closed - Opened by Delayed-Gitification over 1 year ago - 2 comments

#90 - Basecalling slow?

Issue - State: closed - Opened by LauraVP1994 over 1 year ago - 4 comments

#89 - Stereo duplex error on mac M1 ultra and M2

Issue - State: closed - Opened by tgogakos over 1 year ago - 7 comments
Labels: enhancement

#88 - dorado basecaller -> Reads processed: 24900Segmentation fault (core dumped)

Issue - State: closed - Opened by sklages over 1 year ago - 40 comments
Labels: bug

#87 - Fix README.md problems

Pull Request - State: closed - Opened by granek over 1 year ago - 2 comments
Labels: documentation

#86 - RAM needs?

Issue - State: closed - Opened by Kirk3gaard over 1 year ago - 19 comments

#85 - enable proxy settings for download_models

Issue - State: closed - Opened by Bjoernsen over 1 year ago - 2 comments
Labels: enhancement

#84 - 5mC Calling Issue

Issue - State: closed - Opened by samim2111 over 1 year ago - 2 comments

#83 - Missing bases

Issue - State: closed - Opened by tnn111 over 1 year ago - 6 comments

#82 - dorado fails with "CuBLAS error 15"

Issue - State: closed - Opened by tnn111 over 1 year ago - 1 comment

#81 - Pod5 tools don't install on Apple Studio.

Issue - State: closed - Opened by tnn111 over 1 year ago - 3 comments

#80 - Missing library

Issue - State: closed - Opened by KlaMa2 over 1 year ago - 9 comments

#79 - 5hmC modification calling with R10.4.1 models

Issue - State: closed - Opened by assafgrw over 1 year ago - 9 comments

#78 - Dorado crashes with device set to cpu

Issue - State: closed - Opened by BonsonW over 1 year ago - 1 comment
Labels: bug

#77 - dorado crashes partway through basecalling

Issue - State: closed - Opened by jackwadden over 1 year ago - 8 comments
Labels: bug

#76 - Demultiplexing error

Issue - State: closed - Opened by mproberts99 over 1 year ago - 1 comment

#75 - M1 Max -b 0 doesn’t seem to pick actual optimal batch size

Issue - State: closed - Opened by itslittman over 1 year ago - 3 comments
Labels: enhancement

#74 - Problem downloading models

Issue - State: closed - Opened by rmorenoayala over 1 year ago - 17 comments

#73 - dorado to output status like guppy

Issue - State: closed - Opened by Kirk3gaard over 1 year ago - 1 comment
Labels: enhancement

#72 - --resume mode

Issue - State: closed - Opened by Kirk3gaard over 1 year ago - 7 comments
Labels: enhancement

#71 - CUDA error: unrecognized error code

Issue - State: closed - Opened by drk0311 over 1 year ago - 5 comments
Labels: bug

#70 - Windows - Dorado 0.1.1 libwinpthread-1.dll not found System Error

Issue - State: closed - Opened by husamia over 1 year ago - 5 comments

#69 - Error undefined symbol cublasGetSmCountTarget from libcublas.so.11

Issue - State: closed - Opened by dithiii over 1 year ago - 6 comments

#68 - Stereo Duplex sloooooow

Issue - State: closed - Opened by adbeggs over 1 year ago - 33 comments
Labels: enhancement

#67 - Segmentation fault

Issue - State: closed - Opened by itslittman over 1 year ago - 3 comments
Labels: bug

#66 - Setting q-score thresholds in dorado?

Issue - State: closed - Opened by incoherentian over 1 year ago - 12 comments
Labels: enhancement

#65 - Chunk size

Issue - State: closed - Opened by itslittman over 1 year ago - 5 comments

#64 - out of memory core dump with [email protected]

Issue - State: closed - Opened by osilander over 1 year ago - 9 comments
Labels: enhancement

#63 - gmake: *** [Makefile:166: all] Error 2

Issue - State: closed - Opened by itslittman over 1 year ago - 17 comments

#62 - The size of tensor a (16) must match the size of tensor b (4) at non-singleton dimension 0

Issue - State: closed - Opened by sarah872 over 1 year ago - 3 comments
Labels: bug

#61 - cmake Error

Issue - State: closed - Opened by kullrich over 1 year ago - 2 comments

#60 - stereo duplex models not getting downloaded?

Issue - State: closed - Opened by femiliani over 1 year ago - 2 comments

#59 - error when basecalling

Issue - State: closed - Opened by adenochemist over 1 year ago - 1 comment

#58 - m1 neural engine

Issue - State: open - Opened by itslittman over 1 year ago - 5 comments
Labels: question

#57 - CUDAOutOfMemoryError for duplex with 3080ti (12Gb)

Issue - State: closed - Opened by olawa over 1 year ago - 6 comments
Labels: bug

#56 - flag issue when using --modified-bases on osx

Issue - State: closed - Opened by dithiii over 1 year ago - 5 comments

#55 - Future of model training by users

Issue - State: closed - Opened by touala over 1 year ago - 2 comments

#54 - 10.4_e8.1_sup models?

Issue - State: closed - Opened by gallardo-seq over 1 year ago - 1 comment
Labels: question

#53 - Can't open model file?

Issue - State: closed - Opened by JasonJWilliamsNY over 1 year ago - 4 comments

#52 - Dorado for selective sequencing

Issue - State: closed - Opened by hasindu2008 over 1 year ago - 1 comment

#51 - [error] [error] key "qscore" not found in the top-level table while trying to perform basecalling with 5mCG models

Issue - State: closed - Opened by Daniel-Tichy over 1 year ago - 2 comments

#50 - [Question] Best practice after successful dorado run

Issue - State: closed - Opened by Krannich479 over 1 year ago - 2 comments

#49 - Embarassing problem!

Issue - State: closed - Opened by adbeggs over 1 year ago - 7 comments

#48 - PromethION-MinION models

Issue - State: closed - Opened by lucapandolfini over 1 year ago - 2 comments

#47 - FASTQ output for Dorado has missing '+' symbol

Issue - State: closed - Opened by jeplb over 1 year ago - 2 comments

#46 - Dorado 'Failed to open pod5'

Issue - State: closed - Opened by femiliani over 1 year ago - 3 comments

#45 - Dorado basecaller significantly slower than guppy_basecaller on A30 and A100 GPUs

Issue - State: closed - Opened by edoyango over 1 year ago - 21 comments
Labels: question

#44 - multiplexing workaround?

Issue - State: closed - Opened by derekstein over 1 year ago - 3 comments
Labels: enhancement

#43 - Live basecalling benchmark on Apple silicon chips

Issue - State: closed - Opened by marcpaga over 1 year ago - 2 comments

#42 - added initial support for dorado on AGX Orin

Pull Request - State: closed - Opened by EpiSlim over 1 year ago - 1 comment

#41 - AttributeError: module 'collections' has no attribute 'Iterable'

Issue - State: closed - Opened by derekstein over 1 year ago - 1 comment

#40 - Download models code 200

Issue - State: closed - Opened by husamia over 1 year ago - 5 comments
Labels: bug

#39 - RNA model?

Issue - State: closed - Opened by itslittman over 1 year ago - 2 comments
Labels: enhancement

#38 - How to acquire Remora models in the toml format that Dorado expects as input?

Issue - State: closed - Opened by oneillkza over 1 year ago - 8 comments
Labels: enhancement

#37 - Error - no kernel image is available for execution on the device

Issue - State: closed - Opened by oneillkza over 1 year ago - 7 comments

#36 - Jetson Orin Support

Issue - State: closed - Opened by mcrone over 1 year ago - 2 comments
Labels: enhancement

#35 - Reads basecalled: Metal command buffer execution failed

Issue - State: closed - Opened by vdejager over 1 year ago - 3 comments
Labels: bug

#34 - Bonito vs dorado

Issue - State: closed - Opened by christopher-vollmers over 1 year ago - 6 comments

#33 - macos binary - quits on startup

Issue - State: closed - Opened by martinleach over 1 year ago - 6 comments
Labels: enhancement

#32 - output metadata

Issue - State: closed - Opened by ziphra over 1 year ago - 2 comments
Labels: question

#31 - docker image available?

Issue - State: closed - Opened by vdejager over 1 year ago - 4 comments
Labels: question

#30 - What about AMD cards?

Issue - State: closed - Opened by billytcl over 1 year ago - 1 comment

#29 - dump contents of pod5 dir to debug windows failure

Pull Request - State: closed - Opened by 0x55555555 over 1 year ago

#28 - Software download issues

Issue - State: closed - Opened by pwh124 over 1 year ago - 4 comments

#27 - Compilation Error: conflicting declaration

Issue - State: closed - Opened by singagan almost 2 years ago - 2 comments

#26 - M1 Pro: "Metal command buffer execution failed: 5, try #2..."

Issue - State: closed - Opened by mshamash almost 2 years ago - 2 comments

#25 - Dorado performance compared to Guppy

Issue - State: closed - Opened by hasindu2008 about 2 years ago - 13 comments

#24 - unstable CPU frequency M1 pro with metal

Issue - State: closed - Opened by iframst about 2 years ago - 2 comments

#23 - Avoid thread resetting in BasecallerNode

Pull Request - State: closed - Opened by EpiSlim about 2 years ago - 1 comment

#22 - Are PromethION models implemented?

Issue - State: closed - Opened by andreaswallberg about 2 years ago - 3 comments

#21 - Error 2

Issue - State: closed - Opened by hamid89 about 2 years ago - 7 comments

#20 - Is the dependent package koi going to be released open source?

Issue - State: closed - Opened by hasindu2008 about 2 years ago - 3 comments

#19 - SLOW5 support for dorado

Pull Request - State: closed - Opened by hiruna72 about 2 years ago - 1 comment

#18 - A fix for int overflow issue

Pull Request - State: closed - Opened by hiruna72 about 2 years ago
Labels: enhancement

#17 - Gh macos builds

Pull Request - State: closed - Opened by iiSeymour about 2 years ago

#16 - Windows builds

Pull Request - State: closed - Opened by iiSeymour about 2 years ago

#15 - pre-commit action

Pull Request - State: closed - Opened by iiSeymour about 2 years ago

#14 - Assertion failed: (ptr != nullptr), function mtl_for_tensor, file metal_utils.cpp, line 138.

Issue - State: closed - Opened by thomasvangurp about 2 years ago - 3 comments
Labels: bug

#13 - Failed to find the kernel: lstm_simd_768_fwd_16

Issue - State: closed - Opened by thomasvangurp about 2 years ago - 2 comments
Labels: bug

#12 - Building on mac osx

Issue - State: closed - Opened by thomasvangurp about 2 years ago - 1 comment
Labels: documentation

#11 - Use pre-commit hooks for code-formatting

Pull Request - State: closed - Opened by EpiSlim about 2 years ago - 1 comment
Labels: enhancement

#10 - There was an error while I was executing the command "cmake --build cmake-build --config Release -- -j" in jetson orin

Issue - State: closed - Opened by lxq-iang about 2 years ago - 5 comments
Labels: enhancement

#9 - what's the GPU memory utilization rate? Does it depend on read length?

Issue - State: closed - Opened by avilella about 2 years ago - 6 comments
Labels: question

#8 - Adding support for clang-format

Pull Request - State: closed - Opened by EpiSlim about 2 years ago - 3 comments

#7 - Assertion failed: (ptr != nullptr), function mtl_for_tensor, file metal_utils.cpp, line 138.

Issue - State: closed - Opened by mjfos2r about 2 years ago - 6 comments
Labels: bug

#6 - Correct parameter format to specify multi-GPUs

Issue - State: closed - Opened by hasindu2008 about 2 years ago - 3 comments

#5 - CUDAOutOfMemoryError on A100

Issue - State: closed - Opened by vdejager about 2 years ago - 3 comments

#4 - CentOS builded instructions needed

Issue - State: closed - Opened by vellamike about 2 years ago - 3 comments
Labels: documentation, enhancement

#3 - Compile issues

Issue - State: closed - Opened by adbeggs about 2 years ago - 39 comments

#2 - comment for README.md

Issue - State: closed - Opened by matthewlinks about 2 years ago - 1 comment

#1 - GitHub actions

Pull Request - State: closed - Opened by iiSeymour about 2 years ago
Labels: enhancement

GitHub / nanoporetech/dorado issues and pull requests