atlas

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Hello, I'm trying to run the test data provided with metagenome-atlas. I just tried the code from getting started. atlas init --db-dir databases test_reads >> all.out.txt 2>&1 atlas run all...

ChristophKnapp

I have added GUNC and BUSCO support. Please review. Thanks!

trickovicmatija

Error in rule build_qc_report:

9

Hello, Although the ATLAS ran with test data, I encountered this error. I use this command to start the pipeline `atlas run qc -j 20 --conda-frontend mamba --profile cluster` Some...

omrctnr

Upgrading to CheckM2

2

Are there plans to replace CheckM1 with CheckM2 in ATLAS? https://www.biorxiv.org/content/10.1101/2022.07.11.499243v1.full

bcpd

`atlas init-public`doesn't work.

1

Unfortunately I based this part on scripts that interact NCBI Trace, which was discontinued in June 2022. Apparently it is very complicated to get the right data from NCBI. I...

SilasK

Error in rule run_megahit

1

- I checked and didn't found a related issue,e.g. while typing the title - ** I got an error in the following rule(s):** ` run_megahit ` - I checked the...

Nachida08

Error in rule DRAM_annotate

5

Hi Silas, I need your help identifying a missing database while running `rule DRAM_annotate`. I am using atlas on a computing node that don't have access to internet, so I...

HamzaMbareche

Error in "binning.smk" and snakemake "returned non-zero exit status 1"

3

Hi, I'm having trouble with the binning step, a couple of different error codes coming up. The first of several errors appear to be related to "No columns to parse...

akbyers

Error in rule run_dram

17

- [x] I checked and didn't found a related issue,e.g. while typing the title - [x] ** I got an error in the following rule(s):** ` ` run_dram dlopen: cannot...

bcpd

Error in rule build_bin_report

1

- [x] I checked and didn't found a related issue,e.g. while typing the title - [x] ** I got an error in the following rule(s):** `build_bin_report ` - [x] I...

cmorganl