search

metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
377 stars 99 forks source link

BinGroup error when start running #741

Open hbyaoherbert opened 5 days ago

hbyaoherbert commented 5 days ago

I install atlas with conda (Atlas version 2.19) I have 8 samples. Each pair-end sample is composed of _1.fastq and _2.fastq. The input folder fqinput contains files: SRR12072177.clean_1.fastq SRR12072184.clean_1.fastq SRR12072202.clean_1.fastq SRR12072177.clean_2.fastq SRR12072184.clean_2.fastq SRR12072202.clean_2.fastq SRR12072179.clean_1.fastq SRR12072190.clean_1.fastq SRR12072204.clean_1.fastq SRR12072179.clean_2.fastq SRR12072190.clean_2.fastq SRR12072204.clean_2.fastq SRR12072180.clean_1.fastq SRR12072192.clean_1.fastq SRR12072180.clean_2.fastq SRR12072192.clean_2.fastq

when I run "atlas init -w atlastest fqinput it says: [Atlas] INFO: I inferred that _1 and _2 distinguish paired end reads. [Atlas] INFO: Found 8 samples [Atlas] ERROR: If you want to use co-binning, you should have at least 5-10 samples per bin group.

And when I continue to run " atlas run -w atlastest/ qc", it just says BinGroup too small (I have 8 samples in a Bingroup) BinGroupSizeError in file /home/hbyao/miniforge3/envs/lucaprot/lib/python3.9/site-packages/atlas/workflow/rules/sample_table.smk, line 4: BinGroup too small File "/home/hbyao/miniforge3/envs/lucaprot/lib/python3.9/site-packages/atlas/workflow/Snakefile", line 40, in File "/home/hbyao/miniforge3/envs/lucaprot/lib/python3.9/site-packages/atlas/workflow/rules/sample_table.smk", line 4, in File "/home/hbyao/miniforge3/envs/lucaprot/lib/python3.9/site-packages/atlas/sample_table.py", line 142, in validate_bingroup_size File "/home/hbyao/miniforge3/envs/lucaprot/lib/python3.9/site-packages/atlas/sample_table.py", line 94, in validate_bingroup_size_cobinning

Atlas version 2.19

SilasK commented 3 days ago

Seems I have a mismatch between the limit that is warned and one that is tested.

I suggest you to put everithing in one bin group. This should be the case, but check the sample.tsv and use metabat as final_binner in the config file. This will give you cross mapping. This should give the best results for this smallish dataset.