Thank you very much for your excellent work, which has solved the issue of SparCC running slowly. However, I encountered some problems when running FastSpar with my own dataset, and I would like to ask for your advice:
1、When I ran the following command:
nohup parallel fastspar --otu_table {}
--correlation bootstrap_correlation/cor_{/}
--covariance bootstrap_correlation/cov_{/}
-i 5 ::: bootstrap_counts/* \ > log/A_parallel.log 2>&1 &
I received warnings such as:
Warning: the following OTUs have only one unique permutation and it is recommended to remove them from this analysis:
bac_86bec507e60bbb78d6ae26be50edfc88 (row 603)
bac_163972b7cbc5b0b875854c18d9b100a7 (row 769)
...
I am not sure whether this indicates a problem with my dataset, but I did find 1000 cor and cov files generated in the bootstrap_correlation folder. Then, following the example code in the tutorial, I was able to run it normally and obtain the results.
If you need more detailed information about my setup or data, I would be happy to provide it. I look forward to your guidance.
Thank you very much for your excellent work, which has solved the issue of SparCC running slowly. However, I encountered some problems when running FastSpar with my own dataset, and I would like to ask for your advice:
1、When I ran the following command:
I received warnings such as:
Warning: the following OTUs have only one unique permutation and it is recommended to remove them from this analysis:
bac_86bec507e60bbb78d6ae26be50edfc88 (row 603)
bac_163972b7cbc5b0b875854c18d9b100a7 (row 769)
...
I am not sure whether this indicates a problem with my dataset, but I did find 1000 cor and cov files generated in the bootstrap_correlation folder. Then, following the example code in the tutorial, I was able to run it normally and obtain the results.
If you need more detailed information about my setup or data, I would be happy to provide it. I look forward to your guidance.