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Dear cactus developers,
We recently encountered an issue with cactus-hal2maf conversion, when --maximumGapLength >0 (e.g. 50 or 100) is used to allow for the gaps in reference (hg38) sequence in al…
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## Expected Behavior
Recently when we attempted to run AF2 on a complex but failed with following error message. We then test it with a notebook we ran before and same error was generated. Please hel…
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**Are you using the latest release?**
I'm using the latest version installed from conda
**Describe the bug**
I ran the command
funannotate test -t predict
and it stops with the err…
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I am running `hmmbuild` on a Stockholm alignment. My input alignment file has an error, and when I run `hmmbuild test.hmm alignment.so`, I get:
```
Error: Oops. Wait. I need name annotation on each …
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Details:
```
234 25.70 8.70 2.27 FBgn0040071 32795 33001 (1678) Jockey-3_DGri#LINE/Jockey 3207 3426 (1287) m_b557s001i5 6658
FBgn0040071 32795 CCAACACCAGCAGCAACAGCAGCCTTCGCAGCCGCA----TAG…
BioWu updated
6 years ago
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Hi,
I have been receiving the following error while executing miRDP2-v1.1.4_pipeline.bash even after formatting the input fasta files:
Use of uninitialized value $id in hash element at bin/scripts…
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@baoxingsong Hello!
I'm pleased to have a seamless experience with your software, but I do have some queries while using it. How can I utilize pairwise alignments to achieve multiple sequence align…
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Hello there,
I have previously used BUSTED-PH successfully on ~500 seqs. Now, I was trying to improve the analysis for a publication and I managed to get up to ~1500 seqs. However, after running for …
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Dear,
I want to run the PASA alignment assembly pipeline using a very genome which has very long trons such as longer than 20kb. I run the pipeline, some errors occur, I want to know whether this err…
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Note to developer:
The extension step (nucleotide level alignment) is the bottleneck in strobealign. There are different three ways to reduce this:
1. Direction 1 (change the alignment module):
…