You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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
The text was updated successfully, but these errors were encountered:
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.
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
The text was updated successfully, but these errors were encountered: