Haochen Zhang

RemoteSSH hangs at checking "/.vscode-server/XXXX.log and /.vscode-server/XXXX.pid" for a running server

6

VS-Code RemoteSSH was working perfectly on my remote server until recently, when this issue started happening occasionally and getting back to normal after a couple of days (probably the previous...

Mutect2 extremely slow in force-calling mode

2

## Bug Report ### Affected tool(s) or class(es): Mutect2 ### Affected version(s) gatk 4.2.5 ### Description Like most use cases, I acquired a high-confidence, "consensus" VCF from a large batch...

bcftools fails to genotype MNP/indels from targeted-sequencing reads

4

Hi, Given a list of known alleles, I was trying to genotype REF/ALT read counts in some samples' BAM files. Relevant to the issue below is that these are libraries...

Python API issue

2

Hi Rick, I have been running lots of samples through the Python API and it has been working quite well. Thanks again for providing this amazing tool. I recently ran...

cmake compilation error

1

Hey! Thanks for writing the tool. I ran the compilation through cmake and got the following error on `CMakeFiles/sciphi.dir/src/findBestTrees.cpp.o` Here is the more detailed log: ``` [ 95%] Building CXX...

### Prerequisites + [x] Have you read [Feedback](https://guangchuangyu.github.io/ggtree/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [x] make sure your are using the latest release version * [x] read the [documents](https://yulab-smu.github.io/treedata-book/) * [x]...

Hi! Thanks for developing this tool! I was just wondering if there is any way of adding HTML formatting to face label texts?

MOSEK in one Conda environment causing error in another

1

Details for the issue -------------------- #### What did you do? I have two Conda environment: `snakemake`- I set up this one first and had been using it without issue. It...

I am using R 4.2.2, on x86_64-apple-darwin17.0 (64-bit). Tried installing `hdp` but got an error similar to the issue mentioned here: https://stackoverflow.com/questions/62077330/ld-error-when-installing-hdp-package-in-r Thanks in advance for any help! log: ```...

Incorporate indel?

6

Hi, Thanks for writing this amazing tool! I just wonder if there's any plan to incorporate indel into the tool? I thought that could make it applicable to more general...