Spades.log file explanation
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3.2 years ago
K.Gee ▴ 40

Hello everyone, I am trying to find the average coverage from a genome. I used Spades for assembling the raw reads with k-mers sizes of 21, 55, 77, 99, and 127

Reading Spades's manual, I found that the average coverage is calculated in a file called Spades.log. I used the command below,

grep -A1 average spades.log

and I got the following results:

 0:01:04.922    64M / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:01:04.924    64M / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 270.591
--
  0:00:25.204    64M / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:00:25.206    64M / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 264.149
--
  0:00:24.370   136M / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:00:24.372   136M / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 253.698
--
  0:00:22.537   144M / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:00:22.538   144M / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 242.892
--
  0:00:22.398   140M / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:00:22.400   140M / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 226.695
--
  0:00:25.091   120M / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:00:25.092   120M / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 195.146

Can anybody explain to me what is the number next to M/9G ? Also, what is the average coverage from the above 5 values that should I consider as “correct” ?

Thank you in advance.

Spades • 2.4k views
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120M / 9G - RAM usage

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Thanks for the answer. Is it possible to explain to me briefly the principle of selecting this option

:00:25.092 120M / 9G INFO General (simplification.cpp : 476) Average coverage = 195.146

for the average coverage over the others?

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It's just for example. All second column is RAM usage.

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οκ I see!!!

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