Daniel Anderson

Error when using make -j4

3

Hello, I am a Mac user and appear to have successfully compiled using GCC. However, when I run make -j4 I get the following errors: ``` /Users/danielanderson/cobs/cobs/construction/classic_index.cpp: In function 'void...

matOptimize crashes when samples are numerically named

1

Hi! I am using Usher and matOptimize as part of a simulation pipeline and have noticed matOptimize errors out when sample names are numerical, as shown below, despite the sample...

Incorrect annotation of one gene as another due to tight clustering of minimizer hits (with minimal example)

1

Hey Leandro! I have been taking a look at cases where Pandora incorrectly annotates on gene as another. I took the first allele in each MSA that build my panRG...

Hey Leandro! This is another issue related to #332. I have noticed there are quite a few cases where Pandora incorrectly annotates one gene as another and there are no...

Error: Prefilter & Search step died with mmseqs 15.6f452 easy-cluster

2

## Expected Behavior mmseqs easy-cluster should finish without errors. ## Current Behavior ``` Query database size: 19552 type: Nucleotide Estimated memory consumption: 8G Target database size: 9776 type: Nucleotide tmp/3198441352783276465/clu_tmp/13016959338117486175/nucleotide_clustering.sh:...

Request for new release

1

Hello @leoisl , Would it be easy for you to make a new release for Pandora reflecting the changes we made to improve read level gene calling accuracy? It would...

0 depth reported across many genes in the pandora consensus

1

Putting this here as a reminder until I am able to get a minimal example showing this. It seems that the quality string in the pandora consensus file says that...