Siddharth Uppal

Hey @ktmeaton thanks a lot for your help. I tried the following 2 approaches: 1. conda install -c bioconda/label/cf201901 vt==2015.11.10 2. Naming my `bam` file same as the `@RG` tag...

Having the same problem with v3.14.1 and specifically with `--meta` mode. Problem persist after using `--continue` as well.

@vasudhajain29 I remember this error popping up when there was something funny with my reads. In my case, I had concatenated two different pairs of sequencing runs and was trying...

@Aiswarya-prasad I think I just ended up using `Megahit` to analyze the reads. However, you can also just use normal `SPades` instead of `metaSPades`. The results are usually comparable.

PhyloPhlan does not generate bootstrap values by itself, you'll have to use the alignment file generated by PhyPhlan to create your tree with bootstrap values. An example command might be:...

@HRGV, I was able to complete the pipeline using `skip_emirge` option. Do you think the above error an emirge bug or a PhyloFlash bug? I was unable to install standalone...

Not sure if it's completely resolved. I'm using the latest version of snakemake (7.20.0) and still facing the `FileExistsError`

No worries. Currently, I'm using a simple hack of removing the directories in the snakefile before executing DRAM. A quick fix for you guys could be to include a `--force`...