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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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error while running on custom media #16

Closed nbutyrate closed 6 years ago

nbutyrate commented 6 years ago

Hi I am trying to run carveme on a custom media list , here is the error

carve genome.faa --gapfill TSB --mediadb mylibrary.tsv

Medium X not in database, ignored. Medium Y not in database, ignored. Medium Z not in database, ignored.

my library looks like this

medium description compound name
TSB Tryptone broth (anaerobic) ala__L L-Alanine
TSB Tryptone broth (anaerobic) cysi__L L Cystine C6H12N2O4S2
TSB Tryptone broth (anaerobic) his__L L-Histidine
TSB Tryptone broth (anaerobic) lys__L L-Lysine
TSB Tryptone broth (anaerobic) pro__L L-Proline
TSB Tryptone broth (anaerobic) trp__L L-Tryptophan
TSB Tryptone broth (anaerobic) arg__L L-Arginine
TSB Tryptone broth (anaerobic) ile__L L-Isoleucine
TSB Tryptone broth (anaerobic) met__L L-Methionine
TSB Tryptone broth (anaerobic) ser__L L-Serine
TSB Tryptone broth (anaerobic) tyr__L L-Tyrosine
TSB Tryptone broth (anaerobic) gly Glycine
TSB Tryptone broth (anaerobic) ile__L L-Isoleucine
TSB Tryptone broth (anaerobic) phe__L L-Phenylalanine
TSB Tryptone broth (anaerobic) thr__L L-Threonine
TSB Tryptone broth (anaerobic) val__L L-Valine
TSB Tryptone broth (anaerobic) glc__D D-Glucose
TSB Tryptone broth (anaerobic) na1 Sodium
TSB Tryptone broth (anaerobic) cl Chloride
TSB Tryptone broth (anaerobic) k Potassium

Please let me know how to correct this

cdanielmachado commented 6 years ago

Hi, You are invoking the command correctly, and your library seems fine. I just do not understand where medium X, Y Z comes from.

Could you please send me your media library file, so I can try to replicate the error?

nbutyrate commented 6 years ago

sorry for the confusion, i pasted a mix of two commands,

here is what i did

carve PAN_pro.faa --gapfill TSB --mediadb media.tsv Failed to gapfill model for medium TSB

attached is my media file for TSB my_media.zip

however, its running for LB using media file from the carveme github page

carve PAN_pro.faa --gapfill LB --mediadb media_orignal.tsv

cdanielmachado commented 6 years ago

Failed to gapfill model for medium TSB means there is no possible solution to make the organism grow on that medium.

I can see that your medium lacks many trace elements (iron, magnesium, zinc, etc), which are necessary for biomass formation.

You can add all the trace elements from our M9 formulation and repeat the reconstruction. In principle it should work:

https://github.com/cdanielmachado/carveme/blob/master/carveme/data/input/media_db.tsv