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Hello everyone,
I was performing the assembly based on 30 GB of N50 approximately 25kB reads, putting the "readLength=30000" since I expected a lot of coverage and my genome is pretty small (and re…
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I need to memory profile per sample rules to figure out what is the optimal mem_gb to set.
jfear updated
3 years ago
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Hello,
Does XGMix work with imputed data as the query file? I am currently getting:
'initializing apriori reference subpop across CRF... Failed allocating memory at load-input.cpp:680 (8.2 Mb)'
…
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Hello,
I am running canu 2.1.1 on a 2.7 Gb highly heterozygous plant genome, starting from ONT reads (N50 about 50 kb, 75x coverage, or 37x per allele). The command used is
`canu -d Sikem_ONT_EC …
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Hi,
I’m having some issues initialising particles with position_initialization and momentum_initialization as numpy arrays, in the following script:
[test.zip](https://github.com/SmileiPIC/Smil…
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**Environment:**
1. Framework: PyTorch
2. Framework version: 1.7.1
3. Horovod version: 0.21.3
4. MPI version: openmpi/4.0.1
5. CUDA version: 11.2
6. NCCL version: 2.7.08
7. Python version: 3.…
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**Snakemake version**
snakemake 5.32.2
**Describe the bug**
I used snakemake on a cluster, the rule is:
_rule mapq_filter:
input:
"output/mapped/{sample}-{rep}-{unit}…
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I develop bioinformatics pipelines as my job. Sun GridEngine(SGE) is used to dispatch computation intensive jobs of a pipeline to a cluster of compute nodes. Currently, I am trying to build a mini-too…
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Currently the credentials for ssh-ing into remote clusters (SGE/Slurm) have to be provided in the `.toml` config file in plain text. This is really bad for security reasons. Use some form of encryptio…
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We are using canu 2.1.1 on Linux with SGE:
`canu -d Sikem_ONT_EC2 -p error_correct minReadLength=15000 genomeSize=5.4g corMaxEvidenceErate=0.15 corMhapFilterThreshold=0.0000000002 corMhapOptions="--t…