Entering edit mode
5.3 years ago
little_more
▴
70
I'm using MGRA server (http://mgra.cblab.org/) to reconstruct rearrangement history but it returns an error. I hope someone here has used this server and knows what is wrong.
Grimm file:
> GCA_000027125.1
-4 +33 -36 +29 -23 +27 -20 +5 -18 -9 +21 -32 -2 -16 +3 -31 -14 +39 -38 +11 -30 +13 -12 -15 +25 +37 -34 +19 -10 +17 -22 +8 -35 +24 -7 -1 +6 -26 +28 $
>GCA_000219515.3
-4 +33 -36 +29 -23 +27 -20 +5 -18 -9 +21 -32 -2 -16 +3 -31 -14 +39 -38 +11 -30 +13 -12 -15 +25 +37 -34 +19 -10 +17 -22 +8 -35 +24 -7 -1 +6 -26 +28 $
>GCA_000599665.1
-35 +24 -7 -1 +6 -26 +28 -4 +33 -36 +29 -23 +27 -20 +5 -18 -9 +21 -32 -2 -16 +3 -31 -14 +39 -38 +11 -30 +13 -12 -15 +25 +37 -34 +19 -10 +17 -22 +8 $
>GCA_001890365.1
-7 -1 +6 -26 +28 -4 +33 -36 +29 -23 +27 -20 +5 -18 -9 +21 -32 -2 -16 +3 -31 -14 +39 -38 +11 -30 +13 -12 -15 +25 +37 -34 +19 -10 +17 -22 +8 -35 +24 $
>GCA_001900295.1
-15 +25 +37 -34 +19 -10 +17 -22 +8 -35 +24 -7 -1 +6 -26 +28 -4 +33 -36 +29 -23 +27 -20 +5 -18 -9 +21 -32 -2 -16 +3 -31 -14 +39 -38 +11 -30 +13 -12 $
>GCA_001900315.1
+7 -24 +35 -8 +22 -17 +10 -19 +34 -37 -25 +15 +12 -13 +30 -11 +38 -39 +14 +31 -3 +16 +2 +32 -21 +9 +18 -5 +20 -27 +23 -29 +36 -33 +4 -28 +26 -6 +1 $
>GCA_002011985.1
-38 +11 -30 +13 -12 -15 +25 +37 -34 +19 -10 +17 -22 +8 -35 +24 -7 -1 +6 -26 +28 -4 +33 -36 +29 -23 +27 -20 +5 -18 -9 +21 -32 -2 -16 +3 -31 -14 +39 $
>GCA_002012045.1
-20 +5 -18 -9 +21 -32 -2 -16 +3 -31 -14 +39 -27 +23 -29 +36 -33 +4 -28 +26 -6 +1 +7 -24 +35 -8 +22 -17 +10 -19 +34 -37 -25 +15 +12 -13 +30 -11 +38 $
>GCA_002142675.1
-12 -15 +25 +37 -34 +19 -10 +17 -22 +8 -35 +24 -7 -1 +6 -26 +28 -4 +33 -36 +29 -23 +27 -20 +5 -18 -9 +21 -32 -2 -16 +3 -31 -14 +39 -38 +11 -30 +13 $
>GCA_002164635.3
+2 +32 -21 +9 +18 -5 +20 -27 +23 -29 +36 -33 +4 -28 +26 -6 +1 +7 -24 +35 -8 +22 -17 +10 -19 +34 -37 -25 +15 +12 -13 +30 -11 +38 -39 +14 +31 -3 +16 $
>GCA_002164645.2
-37 -25 +15 +12 -13 +30 -11 +38 -39 +14 +31 -3 +16 +2 +32 -21 +9 +18 -5 +20 -27 +23 -29 +36 -33 +4 -28 +26 -6 +1 +7 -24 +35 -8 +22 -17 +10 -19 +34 $
>GCA_002278115.2
-37 -25 +15 +12 -13 +30 -11 +38 -39 +14 +31 -3 +16 +2 +32 -21 +9 +18 -5 +20 -27 +23 -29 +36 -33 +4 -28 +26 -6 +1 +7 -24 +35 -8 +22 -17 +10 -19 +34 $
>GCA_002310595.1
-19 +34 -37 -25 +15 +12 -13 +30 -11 +38 -39 +14 +31 -3 +16 +2 +32 -21 +9 +18 -5 +20 -27 +23 -29 +36 -33 +4 -28 +26 -6 +1 +7 -24 +35 -8 +22 -17 +10 $
>GCA_002310615.1
-19 +34 -37 -25 +15 +12 -13 +30 -11 +38 -39 +14 +31 -3 +16 +2 +32 -21 +9 +18 -5 +20 -27 +23 -29 +36 -33 +4 -28 +26 -6 +1 +7 -24 +35 -8 +22 -17 +10 $
>GCA_002310655.1
-19 +34 -37 -25 +15 +12 -13 +30 -11 +38 -39 +14 +31 -3 +16 +2 +32 -21 +9 +18 -5 +20 -27 +23 -29 +36 -33 +4 -28 +26 -6 +1 +7 -24 +35 -8 +22 -17 +10 $
>GCA_002591135.1
+31 -23 +27 -20 +5 -18 -9 +21 -32 -2 -16 +3 -29 +36 -33 +4 -28 +26 -6 +1 +7 -24 +35 -8 +22 -17 +10 -19 +34 -37 -25 +15 +12 -13 +30 -11 +38 -39 +14 $
>GCA_002787215.1
-30 +13 -12 -15 +25 +37 -34 +19 -10 +17 -22 +8 -35 +24 -7 -1 +6 -26 +28 -4 +33 -36 +29 -23 +27 -20 +5 -18 -9 +21 -32 -2 -16 +3 -31 -14 +39 -38 +11 $
>GCA_002788115.1
+18 -2 -16 +3 -31 -14 +39 -38 +11 -30 +13 -12 -15 +25 +37 -34 +19 -10 +17 -22 +8 -35 +24 -7 -1 +6 -26 +28 -4 +33 -36 +29 -23 +27 -20 +5 +32 -21 +9 $
>GCA_002925525.1
-2 -16 +3 -31 -14 +39 -38 +11 -30 +13 -12 -15 +25 +37 -34 +19 -10 +17 -22 +8 -35 +24 -7 -1 +6 -26 +28 -4 +33 -36 +29 -23 +27 -20 +5 -18 -9 +21 -32 $
>GCA_002968735.1
-22 +8 -35 +24 -7 -1 +6 -26 +28 -4 +33 -36 +29 -23 +27 -20 +5 +32 -21 +9 +18 -2 -16 +3 -31 -14 +39 -38 +11 -30 +13 -12 -15 +25 +37 -34 +19 -10 +17 $
>GCA_003030245.1
-6 +1 +7 -24 +35 -8 +22 -17 +10 -19 +34 -37 -25 +15 +12 -13 +30 -11 +38 -39 +14 +31 -3 +16 +2 +32 -21 +9 +18 -5 +20 -27 +23 -29 +36 -33 +4 -28 +26 $
>GCA_003180995.1
-32 -2 -16 +3 -29 +36 -33 +4 -28 +26 -6 +1 +7 -24 +35 -8 +22 -17 +10 -19 +34 -37 -25 +15 +12 -13 +30 -11 +38 -39 +14 +31 -23 +27 -20 +5 -18 -9 +21 $
>GCA_003410275.1
-33 +4 -28 +26 -6 +1 +7 -24 +35 -8 +22 -17 +10 -19 +34 -37 -25 +15 +12 -13 +30 -11 +38 -39 +14 +31 -3 +16 +2 +32 -21 +9 +18 -5 +20 -27 +23 -29 +36 $
>GCA_003571785.1
-25 +15 +12 -13 +30 -11 +38 -39 +14 +31 -23 +27 -20 +5 +32 -21 +9 +18 -2 -16 +3 -29 +36 -33 +4 -28 +26 -6 +1 +7 -24 +35 -8 +22 -17 +10 -19 +34 -37 $
Tree:
(((((GCA_003030245.1,((((GCA_000027125.1,GCA_002278115.2),(GCA_002011985.1,GCA_001900315.1)),((GCA_002310615.1,GCA_000219515.3),GCA_003410275.1)),(((GCA_002310595.1,(GCA_001890365.1,(GCA_001900295.1,GCA_002012045.1))),GCA_002310655.1),GCA_000599665.1))),(GCA_002925525.1,((GCA_003571785.1,GCA_003180995.1),GCA_002787215.1))),GCA_002591135.1),((GCA_002164645.2,GCA_002164635.3),GCA_002788115.1)),GCA_002968735.1,GCA_002142675.1);
The error I get:
ERROR: Unknown genome in (sub)tree: GCA_002968735.1,GCA_002142675.1
Although the genomes are present in grimm file.
