Longhao Jia

We want to use GDC on large graph with more than 200,000 nodes, but directly calculating T^{-1} and expm(T) is very show. We also notice your advice: [How to use...

Error with "circular-linear-split.py"

1

[2022-08-15 16:36 INFO] Executing: snakemake --snakefile /home1/jialh/tools/miniconda3/envs/vs2/lib/python3.6/site-packages/virsorter/Snakefile --directory /share/inspurStorage/home3/ZXMGroup/VIROME/G3compare/results/04UHGG/test.out --jobs 4 --configfile /share/inspurStorage/home3/ZXMGroup/VIROME/G3compare/results/04UHGG/test.out/config.yaml --latency-wait 600 --rerun-incomplete --nolock --conda-frontend mamba --conda-prefix /share/inspurStorage/home1/jialh/human_virome/tools/db/conda_envs --use-conda --quiet all Job counts: count jobs 1 all...

When I want to install ilupp, I get the following error. We tried searching for a solution via Google, but to no avail. If you can provide some helpful suggestions,...

[2023-06-04T07:45:16Z INFO coverm::contig] In sample 'cdhit_rep_seq.fna/SRR13083091_1.fq.gz', found 0 reads mapped out of 0 total (NaN%)

3

When we run coverm: ```shell /home1/jialh/anaconda3/envs/MAG/bin/coverm contig \ -t 8 -r /home1/jialh/brain/CAGs/CAGs/cdhit_rep_seq.fna \ -1 /home1/jialh/brain/JPN/preprocessing/01_processing/05_sync/SRR13083091_1.fq.gz \ -2 /home1/jialh/brain/JPN/preprocessing/01_processing/05_sync/SRR13083091_2.fq.gz \ --bam-file-cache-directory /home1/jialh/brain/CAGs/CAGs/coverm/SRR13083091_coverm_temp \ --output-file /home1/jialh/brain/CAGs/CAGs/coverm/SRR13083091_gene_abundance.txt ``` We got the next error....

Failed to install DTR-phage-pipeline

5

 After run: ``` conda env create -f environment.yml conda activate DTR-phage-pipeline snakemake --use-conda -p -r -j 10 ``` I got the error, -bash: /home1/jialh/tools/miniconda3/envs/DTR-phage-pipeline/bin/snakemake: /home1/jialh/tools/miniconda3/envs/DTR-phage-pipeline/bin/python3.8: bad interpreter: Invalid argument

I hope to use graph variational autoencoders in weighted biological networks with hundreds of thousands of nodes and millions of edges. FastGAE can help handle such a large network, but...

I got the error 'Segmentation fault (core dumped)' when installing ilma. ``` (pacbio) [jialh@amdnode3 MM_10Plex_42MB_SEQUENCING_DATA_EXPRESS2.0]$ mamba install bioconda::lima Looking for: ['bioconda::lima'] conda-forge/linux-64 Using cache conda-forge/noarch Using cache bioconda/linux-64 Using cache...

torch.cuda.OutOfMemoryError: CUDA out of memory

1

我们注意到，您在论文中使用了ogbn-Arxiv和ogbn-Papers100M等大型数据集，但是在我们自己的服务器上测试时，发现内存超了。 请问您ogbn-Arxiv数据集上训练过程中，内存消耗大概是多少？ 关于运行GraphMAE2或者处理百万节点级别的大规模图，您有什么建议吗？ ```python (graphmb) [jialh@gpu07 GraphMAE2]$ sh 01run_ogbn-arxiv.sh 2024-04-22 21:08:20,721 - INFO - ----- Using best configs from configs/ogbn-arxiv.yaml ----- Namespace(seeds=[0], dataset='ogbn-arxiv', device=0, max_epoch=60, warmup_steps=-1, num_heads=8, num_out_heads=1, num_layers=4, num_dec_layers=1,...

For a real metagenomic dataset that we can not know the true number of bins, how to determine the parameter ‘--n_clusters’ ?

object 'passed_ss_age' not found

1

I got the following errors when running [the ANCOM-BC2 Tutorial](https://bioconductor.org/packages/release/bioc/vignettes/ANCOMBC/inst/doc/ANCOMBC2.html). ```R > df_fig_age = df_age %>% + dplyr::filter(diff_age == 1) %>% + dplyr::arrange(desc(lfc_age)) %>% + dplyr::mutate(direct = ifelse(lfc_age > 0,...