Peter Ebert
Peter Ebert
Hi, I have a question regarding using parental HiFi instead of Illumina data for a trio-phased assembly (all experiments done with recent versions of hifiasm and yak). When doing this,...
Hi, we have used two different hifiasm versions for assembling male genomes. For chrY, we observed that the more recent version (v0.15.2) distributes the chrY sequences between primary and alternate...
Hi, there seems to be a problem running several commands in the form of an anon rule when using Singularity containers. **Snakemake version** 7.12.0 **Describe the bug** The shell command...
Hi, I am using Snakemake v5.9.1, and the following error has been bugging me for quite some time. In a workflow where certain rules have `directory()` as output, updating the...
Hi, I am using sniffles v2.2 and I have a few suggestions regarding the handling of the sample ID: 1. my BAM files have the sample ID in the `SM`...
Hi, **Describe the bug** `AttributeError: module 'MySQLdb' has no attribute 'escape_string'` **To Reproduce** Test run on small dataset with all default CLI parameters (should be shareable upon request) **Expected behavior**...
Hi, no real bug report, just an info to potentially help others who run into similar problems: running the containerized version of Peregrine (tested with v0.1.6.1) with Singularity on infrastructure...
Hi Mikko, if you are interested, I can send you the data (a few gigs) behind this segfault if you want to debug this: ``` HG00733_3_Guppy_4.2.2_prom_MAP-TO_mbg-k5001-w2000.ms20000.ga.log:Signal 11. Read: 58648ef0-bc07-43fa-94b7-495b7161af3b. Seed:...
*Is this a feature request for FCS-adaptor or FCS-GX?* FCS-adaptor (I am using v0.4.0) *Describe the problem you'd like to be solved* Don't fail on sequences
Hi, when running the following command, I get a NameError: ``` vembrane filter --aux chroms=main_chroms.tsv 'CHROM in AUX["chroms"] and "PASS" in FILTER' input.vcf.gz ``` ``` Traceback (most recent call last):...