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chrisquince / DESMAN

De novo Extraction of Strains from MetAgeNomes
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Error when running Desman test: "Infer strains with Desman" #25

Open sacl07 opened 6 years ago

sacl07 commented 6 years ago

Hi, i am doing the tutorial, and i get an error when doing the "Infer strains with Desman" part. Concretely, when running this code: for g in 2 3 4 5 6 7 8; do for r in 0 1 2 3 4; do desman ../Variants/outputsel_var.csv -e ../Variants/outputtran_df.csv -o ClusterEC_${g}_${r} -r 1000 -i 100 -g $g -s $r > ClusterEC_${g}_${r}.out& done; done

The errors that i get in the log files are:

2018-04-10 16:14:58,097:INFO:root:Results created in /home/life/DesmanExample/Example/RunDesman/ClusterEC_2_0 2018-04-10 16:14:58,116:INFO:root:Set fixed seed for random position selection = 238329 2018-04-10 16:14:58,225:ERROR:root:Not enough samples with minimum coverage 0 or variant positions 0. Exiting!

I also get these error messages in the terminal: /home/life/.local/lib/python3.5/site-packages/numpy/core/fromnumeric.py:2957: RuntimeWarning: Mean of empty slice. out=out, **kwargs) ImportError: cannot import name mainImportError: cannot import name main

chrisquince commented 6 years ago

Hi

What has probably gone wrong here is that you have failed to create the outputsel_var.csv file correctly, what does it look like, does it have selected variants and frequencies in each of the samples?

Something like this:

,Position,Sample564_sub-A,Sample564_sub-C,Sample564_sub-G,Sample564_sub-T,Sample767_sub-A,Sample767_sub-C,Sample767_sub-G,Sample767_sub-T,Sample733_sub-A,Sample733_sub-C,Sample733_sub-G,Sample733_sub-T, Sample746_sub-A,Sample746_sub-C,Sample746_sub-G,Sample746_sub-T,Sample548_sub-A,Sample548_sub-C,Sample548_sub-G,Sample548_sub-T,Sample759_sub-A,Sample759_sub-C,Sample759_sub-G,Sample759sub-T,Sample616 sub-A,Sample616_sub-C,Sample616_sub-G,Sample616_sub-T,Sample620_sub-A,Sample620_sub-C,Sample620_sub-G,Sample620_sub-T,Sample803_sub-A,Sample803_sub-C,Sample803_sub-G,Sample803_sub-T,Sample609_sub-A,Samp le609_sub-C,Sample609_sub-G,Sample609_sub-T,Sample710_sub-A,Sample710_sub-C,Sample710_sub-G,Sample710_sub-T,Sample631_sub-A,Sample631_sub-C,Sample631_sub-G,Sample631_sub-T,Sample687_sub-A,Sample687_sub- C,Sample687_sub-G,Sample687_sub-T,Sample712_sub-A,Sample712_sub-C,Sample712_sub-G,Sample712_sub-T,Sample624_sub-A,Sample624_sub-C,Sample624_sub-G,Sample624_sub-T,Sample717_sub-A,Sample717_sub-C,Sample71 7_sub-G,Sample717_sub-T k119_4275_6,43,15,0,4,0,13,0,0,0,32,0,5,0,12,0,0,0,18,0,0,0,33,1,0,0,15,0,7,0,23,0,0,0,35,0,1,0,27,0,0,0,11,0,0,0,8,0,0,0,14,0,0,0,21,0,0,0,29,0,4,0,25,0,2,0 k119_4275_6,82,16,0,0,0,10,0,0,0,31,0,0,0,16,0,0,0,0,0,16,0,33,0,3,0,19,0,0,0,21,0,0,0,33,0,0,0,22,0,3,0,10,0,0,0,12,0,0,0,12,0,2,0,20,0,3,0,31,0,0,0,29,0,0,0 k119_4275_6,88,3,0,14,0,0,0,9,1,6,0,25,0,0,0,17,0,0,0,16,0,0,0,35,0,10,0,9,0,0,0,22,0,1,0,34,0,0,0,28,0,1,0,9,0,1,0,13,0,1,0,14,0,0,0,25,0,26,0,4,0,9,0,20,0 k119_4275_6,97,17,0,0,0,9,0,0,0,30,0,0,0,16,0,1,0,0,0,17,0,31,0,2,0,18,0,0,0,23,0,0,0,39,0,0,0,25,0,6,0,9,0,0,0,14,0,0,0,10,0,2,0,23,0,4,0,25,1,0,0,27,0,0,0 k119_4275_6,103,16,0,0,1,7,0,0,0,26,0,0,5,16,0,0,0,17,0,0,0,33,0,1,0,15,0,0,5,21,0,0,0,35,0,0,2,30,0,0,0,11,0,0,0,12,0,0,1,12,0,0,1,26,0,0,0,24,0,1,2,18,1,0,9 k119_4275_6,106,16,0,0,0,7,0,0,0,26,0,4,0,15,0,0,0,17,0,0,0,33,0,0,0,15,0,5,0,21,0,0,0,31,0,2,0,30,0,0,0,11,0,0,0,12,0,1,0,12,0,1,0,27,0,0,0,25,0,2,0,19,0,10,0 k119_4275_6,148,0,13,0,2,0,7,0,0,0,24,0,6,0,14,0,0,0,12,0,0,0,28,0,0,0,15,0,11,0,25,0,0,0,35,0,2,0,30,0,0,0,15,0,0,0,10,0,1,0,10,0,2,0,30,0,0,0,4,0,24,0,14,0,10 k119_10824_2,6,1,0,12,0,0,0,9,0,0,0,21,0,0,0,17,0,0,0,19,0,0,0,35,0,1,0,15,0,0,0,12,0,0,0,26,0,0,0,24,0,0,0,10,0,0,0,7,0,0,0,7,0,0,0,23,0,7,0,2,0,0,0,17,0 k119_10824_2,100,1,0,20,0,0,0,9,0,2,0,23,0,0,0,16,0,0,0,18,0,0,0,39,0,3,0,16,0,0,0,18,0,0,0,35,0,0,0,21,0,0,0,12,0,0,0,9,0,0,0,6,0,0,0,29,0,2,0,5,0,1,0,15,0 ....

Thanks, Chris