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My workflow failed in a previous run, in which I requested it to stopAfter haplotyping the reads, due to an out-of-memory error (see below if that is useful)
I then allocated more memory to my machin…
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My code keeping using 4GB RAM and getting killed even though I specify minMemory=16. Also gnuplot fails every time.
PBS Script
```
#!/bin/bash
#PBS -P OSR
#PBS -N canu1
#PBS -l select=1:ncpus…
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IGV is a very useful viewer for PacBio long read data, but it could be even better with a few modifications. Ideas to improve support for PacBio data are:
1. **Add a "quick consensus" mode** that onl…
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I have got a pacbio raw data for about 4Gbp plant genome with about 32x coverage. I use the canu 2.0. I used on cluster with only one node (48 CPU core and 126 GB ram)
Firstly, I tried only error c…
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Hello!
I have two questions.
1. using multiple computing nodes
2. failure with useGrid=true
Before telling you the detail, here are the basics settings of my linux server
```
1) I …
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Hi,
I am writing here to seek your opinion on using HapCUT2 to perform phasing genome of a plant that I am interested at. I have a plant genome that I am working on, genome size 400Mb, 11 chromosom…
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Hi @secastel :+1: pHASER has been quite helpful for me. However, I have encountered several issues that would need attention to make this tool better.
**1)** The vcf file output by pHASER isn't qui…
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Hi Stephane,
Many thanks for sharing phaser, great tool! I was wondering if there is any way to get all possible haplotypes for a particular gene, when this is compatible with the input data.
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Dear Stephane,
I am experiencing some problems with Phaser results.
I need to obtain allelic counts for hybrid yeast, and I know the reference sequence of one of its parents.
My pipeline is follo…
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- [x] Update to current version v0.6.3-beta
- [x] add --somatic-filter-expression \"AD < -1 | AF < -1 | ADP > 100000000 | SB < -1 \" \
- [ ] random forest? constitutional?