Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

trouble reading remora models #337

Open
stephrom opened this issue Mar 13, 2023 · 0 comments
Open

trouble reading remora models #337

stephrom opened this issue Mar 13, 2023 · 0 comments

Comments

@stephrom
Copy link

Dear,

I'm trying to run megalodon but I'm stuck when remora models need to be read.

my cmd line is:
megalodon --overwrite
--outputs basecalls mappings mod_mappings per_read_mods mods
--guppy-config dna_r9.4.1_450bps_hac.cfg
--guppy-server-path $guppy_path/guppy_basecall_server
--remora-modified-bases dna_r9.4.1_e8 hac 3.5.1 5mc CG 0
--mod-motif m CG 0
--write-mods-text
--reference $ref
--devices all
--processes $NSLOTS $dir/megalodon_CpG/fast5

error returned:
[16:31:35] Running Megalodon version 2.5.0
[16:31:35] Loading guppy basecalling backend
******************** WARNING [16:31:38:MainProcess:MainThread:model_util.py:491]: Remora model for basecall model version (3.5.1) not found. Using default Remora model for dna_r9.4.1_e8_hac. ********************
******************** WARNING: Remora model for basecall model version (3.5.1) not found. Using default Remora model for dna_r9.4.1_e8_hac. ********************
[16:31:38] No pre-trained Remora model found for this configuration dna_r9.4.1_e8_hac_v3.5.1_5mc_CG_v0.pt at /shared/clssoft/apps/x86_64/megalodon/2.5.0/lib/python3.8/site-packages/remora/trained_models.
Attempting to download dna_r9.4.1_e8_hac_v3.5.1_5mc_CG_v0.pt
[16:31:38] No pre-trained Remora model found for this configuration dna_r9.4.1_e8_hac_v3.5.1_5mc_CG_v0.pt at /shared/clssoft/apps/x86_64/megalodon/2.5.0/lib/python3.8/site-packages/remora/trained_models.
Attempting to download dna_r9.4.1_e8_hac_v3.5.1_5mc_CG_v0.pt
[16:31:40] Model dna_r9.4.1_e8_hac_v3.5.1_5mc_CG_v0.pt downloaded to /shared/clssoft/apps/x86_64/megalodon/2.5.0/lib/python3.8/site-packages/remora/trained_models/dna_r9.4.1_e8_hac_v3.5.1_5mc_CG_v0.pt
[16:31:40] Model dna_r9.4.1_e8_hac_v3.5.1_5mc_CG_v0.pt downloaded to /shared/clssoft/apps/x86_64/megalodon/2.5.0/lib/python3.8/site-packages/remora/trained_models/dna_r9.4.1_e8_hac_v3.5.1_5mc_CG_v0.pt
terminate called after throwing an instance of 'c10::Error'
what(): isTuple() INTERNAL ASSERT FAILED at "/pytorch/aten/src/ATen/core/ivalue_inl.h":931, please report a bug to PyTorch. Expected Tuple but got String
Exception raised from toTuple at /pytorch/aten/src/ATen/core/ivalue_inl.h:931 (most recent call first):
frame #0: c10::Error::Error(c10::SourceLocation, std::string) + 0x42 (0x7fcb09d598b2 in /shared/clssoft/apps/x86_64/megalodon/2.5.0/lib/python3.8/site-packages/torch/lib/libc10.so)
frame #1: + 0x2f850b0 (0x7fcb0d14d0b0 in /shared/clssoft/apps/x86_64/megalodon/2.5.0/lib/python3.8/site-packages/torch/lib/libtorch_cpu.so)
frame #2: + 0x2f873a5 (0x7fcb0d14f3a5 in /shared/clssoft/apps/x86_64/megalodon/2.5.0/lib/python3.8/site-packages/torch/lib/libtorch_cpu.so)
frame #3: torch::jit::SourceRange::highlight(std::ostream&) const + 0x38 (0x7fcb0add7d68 in /shared/clssoft/apps/x86_64/megalodon/2.5.0/lib/python3.8/site-packages/torch/lib/libtorch_cpu.so)
frame #4: torch::jit::ErrorReport::what() const + 0x2c5 (0x7fcb0adb72d5 in /shared/clssoft/apps/x86_64/megalodon/2.5.0/lib/python3.8/site-packages/torch/lib/libtorch_cpu.so)
frame #5: + 0x2b2d7e (0x7fcb1b192d7e in /shared/clssoft/apps/x86_64/megalodon/2.5.0/lib/python3.8/site-packages/torch/lib/libtorch_python.so)
frame #6: + 0x2c6721 (0x7fcb1b1a6721 in /shared/clssoft/apps/x86_64/megalodon/2.5.0/lib/python3.8/site-packages/torch/lib/libtorch_python.so)

frame #47: __libc_start_main + 0xf5 (0x7fcb31482555 in /lib64/libc.so.6)
frame #48: /shared/clssoft/apps/x86_64/megalodon/2.5.0/bin/python() [0x40065e]

Abort (core dumped)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant