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BinGroup error when start running #741

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hbyaoherbert opened this issue Nov 18, 2024 · 1 comment
Open

BinGroup error when start running #741

hbyaoherbert opened this issue Nov 18, 2024 · 1 comment

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@hbyaoherbert
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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
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SilasK commented Nov 20, 2024

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.

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