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Hello,
I have been trying to place them in the tree with pplacer but it fails for memory every time.
I have 512 GB of RAM on this node:
First run on 28 genomes:
slurmstepd: error: Job 9369956 …
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Is there a way to make the .genome file headlessly on the command line? I made a .chrom.sizes file which takes the place of the .genome file but the alignments with annotations would be much preferred…
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Hi,
I have found several bugs when I running the gridss_somatic_filter.R in docker image (version 2.11.1 in quay).
1) Olson database is not installed.
2) Script asks for reference genome, and try…
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I was going to create a PR, but there are some other differences in my fork that shouldn't get merged, so I'll just describe the changes here.
See this commit for reference: https://github.com/rcsb…
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error messgae:
Aligning marker genes with multiple hits in a single bin:
Finished processing 0 of 4463 (0.00%) bins.
Unexpected error:
Traceback (most recent call last):
File "/data2/lcy…
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Hello everyone,
annotation files become bigger and bigger. For example the annotation file for GRCh38 provided by ensembl has around 400MB if uncompressed.
When trying to load such big file igv …
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Talking about this with @andrewkern and @vsbuffalo. Currently, the "Chromosomal inversion" recipe of section 14.4 has a recombination callback that looks like this:
```
recombination() {
if (gen…
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Hello,
I've been trying to adopt this pipeline for some of our labs WGBS data and I thought I had gotten past most of the bugs but I got a new one that has me stumped so I wanted to open an issue,…
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Hi, maybe I'm doing something wrong, but I can't seem to make `bcftools merge --info-rules` flag to behave as I want it to. Here's what I'm doing:
### Build bcftools v1.11
```bash
wget https://gi…
tskir updated
3 years ago
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Run for HBV genome:
```console
python3 -m src.run_simulation temp/run_2022/NC_003977.2_HBV.gb temp/100_tree.newick --outfile temp/out_hbv_0.5.fa --global_rate 0.5
```
![image](https://user-images…