Ali Mirza

Changing the time limit doesn't seem to work properly. I supplied new config rules to the `-c` parameter, such as: ``` process { withName:QIIME2_EXTRACT { cpus = 2 memory =...

I also had set `--max_time` to `500h`. Below is my sbatch script: ``` #!/bin/bash -l #SBATCH --time=3-12:00:00 #SBATCH --nodes=4 #SBATCH --cpus-per-task=8 #SBATCH --mem-per-cpu=4G #SBATCH --error=%x-%j.error #SBATCH --output=%x-%j.out nextflow run main.nf...

I think I got It to work after increasing the number of CPUs but now I have another problem. Apparently It is running out of space "`[Errno 28] No space...

I need to know a couple things about using the gg2 database. When using the process `QIIME2_TRAIN` on the gg2 database, which is a high process job with 1 cpu,...

To reduce memory usage, I will add the parameter `--p-classify--chunk-size 10000` (default 20000) to the `qiime feature-classifier fit-classifier-naive-bayes` plugin in the `modules/local/qiime2_train.nf` module. I'll let you know if it works.

`QIIME2_TRAIN` is dumping data into `/tmp` directory. The process is putting files into `/tmp` and not into my specified `/scratch` directory. The issue is likely due to the `/tmp` folder...

Actually, binding Singularity to the specified directory using `singularity { runOptions...` was essential and specifying `TMP` and `TMPDIR` was not enough. I discovered that the variables (`QIIME2_TMPDIR`, `JOBLIB_TEMP_FOLDER`, etc.) were...

> I was thinking in keep all my taxa for alpha and beta diversity metrics but filtered out these unassigned sequence for my ANCOMBC2 analysis. @DavidRR24 The problem with removing...

Not even the alignment parameters, which is done before error modelling? I am worried that important sequences not aligning to each other because of more variability in the COI gene...

Got it, thank you!