irleader

keyerror when running prediction mode

4

I downloaded mus_musculus.ipc and instanovo.pt. Run the command "python -m instanovo.transformer.predict ms_ninespecies_benchmark/data/ninespecies_updated/mus_musculus.ipc instanovo.pt", the error message is as follows: 100%|██████████████████████████████████████████████████████████████████████████████| 408/408 [1:42:54

Possibility of training the model to predict pepide with modifications

1

Hi, Our dataset have lots of modifications which are important, is it possible to modify the model a bit, such that we can train PepNet from scratch by ourselves to...

Illustration of pretrained model checkpoint

1

Hi, Changelog for release 0.1.4 states: "add checkpoints instanovo.pt trained on HC-PT, and instanovo_yeast.pt fine-tuned on nine-species excluding yeast." After checking the vocab/residues for both model checkpoints: instanovo.pt does not...

Suggested setting for fasta file as input with certain modifications

8

Hi Douwe Schulte, Thanks a lot for developing such a great tool which benefits the whole proteomics community! I am using several de novo peptideing sequencing tools (including casanovo) that...

From output of InstaNovo and InstaNovo+, only peptide-level log probability is available. We would like to use the peptides predicted from InstaNov/InstaNovo+ to do protein assembly, where amino acid probability/score...

combined reads and score/depth calculation

1

When will two peptides be combined into one read? When they have exactly the same sequence (but different modifications are OK)? When calculating match score/ unique match score, will the...

System.OutOfMemoryException

1

">> Error: Exception of type 'System.OutOfMemoryException' was thrown. --> Stacktrace: | System.Text.StringBuilder.ToString() | HtmlGenerator.XmlBuilder`1.ToString() | HtmlGenerator.XmlBuilder`1.Add[T](XmlBuilder`1) ╷ Stitch.HTMLReport.CreateAndSaveAside(AsideType, Int32, Int32, Int32) ╰─ D:\a\stitch\stitch\stitch\Reporting\HTMLReport\Report.cs:line 111 >> Error: One or more errors...

error when provided a single template with more than 12000 proteins

1

"at Stitch.PhylogeneticTree+Tree`1[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]].Remodel[[System.ValueTuple`2[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e],[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]], System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]](System.Func`2) ...... at Stitch.PhylogeneticTree+Tree`1[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]].Remodel[[System.ValueTuple`2[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e],[System.__Canon, System.Private.CoreLib,...