Sean

not working with singularity

1

I have followed the instructions in the readme for downloading the databases but now I'm trying to run camitax on real genomes and I get a lot of errors: ```...

Read count doesn't match expected from extract_kraken_reads.py

1

I am trying to extract the reads from a single taxid at that level (no parents or children). The hierarchy looks like: ``` 0.01 1898 0 P 2732408 Pisuviricota 0.01...

Freebayes implementation missing?

1

The manuscript mentions, "Base quality is optionally determined using FreeBayes [54] to measure read support and mixed alleles." I don't see that option in the v1.2 command line options. Also,...

overwrite 'assembly_summary.txt' prompt

5

Variants of this issue may have been mentioned in other issues, so sorry if it is a duplicate. The standard database build looks like it is trying to `overwrite 'assembly_summary.txt'`...

Since v 2.1.3, parsnp has handled multi-fasta references a produces a vcf with the correct CHROM labels. It seems like the bed file produced by running PhiPack (--recomb-filter) doesn't support...