diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A0QHY3.dssp b/toy_example/data/dssp/A0QHY3.dssp similarity index 99% rename from toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A0QHY3.dssp rename to toy_example/data/dssp/A0QHY3.dssp index f04e750..66b2d76 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A0QHY3.dssp +++ b/toy_example/data/dssp/A0QHY3.dssp @@ -1,4 +1,4 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . +==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2024-03-21 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER 01-JUN-22 . COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A0R756.dssp b/toy_example/data/dssp/A0R756.dssp similarity index 99% rename from toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A0R756.dssp rename to toy_example/data/dssp/A0R756.dssp index aae56be..e8a34e9 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A0R756.dssp +++ b/toy_example/data/dssp/A0R756.dssp @@ -1,4 +1,4 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . +==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2024-03-21 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER 01-JUN-22 . COMPND MOL_ID: 1; MOLECULE: L-ERYTHRULOSE-1-PHOSPHATE ISOMERASE; CHAIN: A . diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A1RUV7.dssp b/toy_example/data/dssp/A1RUV7.dssp similarity index 99% rename from toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A1RUV7.dssp rename to toy_example/data/dssp/A1RUV7.dssp index f2614b3..ab7eccc 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A1RUV7.dssp +++ b/toy_example/data/dssp/A1RUV7.dssp @@ -1,4 +1,4 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . +==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2024-03-21 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER 01-JUN-22 . COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A5FRB6.dssp b/toy_example/data/dssp/A5FRB6.dssp similarity index 99% rename from toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A5FRB6.dssp rename to toy_example/data/dssp/A5FRB6.dssp index 41c5002..bd45460 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/A5FRB6.dssp +++ b/toy_example/data/dssp/A5FRB6.dssp @@ -1,4 +1,4 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . +==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2024-03-21 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER 01-JUN-22 . COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/P72484.dssp b/toy_example/data/dssp/P72484.dssp similarity index 99% rename from toy_example/results/toy_example_2023_12_07_20_58_09/dssp/P72484.dssp rename to toy_example/data/dssp/P72484.dssp index 3537049..d3bd2bb 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/P72484.dssp +++ b/toy_example/data/dssp/P72484.dssp @@ -1,4 +1,4 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . +==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2024-03-21 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER 01-JUN-22 . COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/P9WG42.dssp b/toy_example/data/dssp/P9WG42.dssp similarity index 99% rename from toy_example/results/toy_example_2023_12_07_20_58_09/dssp/P9WG42.dssp rename to toy_example/data/dssp/P9WG42.dssp index 40f253b..70123db 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/P9WG42.dssp +++ b/toy_example/data/dssp/P9WG42.dssp @@ -1,4 +1,4 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . +==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2024-03-21 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER 01-JUN-22 . COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q3KM32.dssp b/toy_example/data/dssp/Q3KM32.dssp similarity index 99% rename from toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q3KM32.dssp rename to toy_example/data/dssp/Q3KM32.dssp index 9ab49d4..1799c0a 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q3KM32.dssp +++ b/toy_example/data/dssp/Q3KM32.dssp @@ -1,4 +1,4 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . +==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2024-03-21 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER 01-JUN-22 . COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q4JCD8.dssp b/toy_example/data/dssp/Q4JCD8.dssp similarity index 99% rename from toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q4JCD8.dssp rename to toy_example/data/dssp/Q4JCD8.dssp index fe6a5c7..6059acc 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q4JCD8.dssp +++ b/toy_example/data/dssp/Q4JCD8.dssp @@ -1,4 +1,4 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . +==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2024-03-21 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER 01-JUN-22 . COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q8Z2Y2.dssp b/toy_example/data/dssp/Q8Z2Y2.dssp similarity index 99% rename from toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q8Z2Y2.dssp rename to toy_example/data/dssp/Q8Z2Y2.dssp index d9a50e9..09beaa9 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q8Z2Y2.dssp +++ b/toy_example/data/dssp/Q8Z2Y2.dssp @@ -1,4 +1,4 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . +==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2024-03-21 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER 01-JUN-22 . COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q8ZJK9.dssp b/toy_example/data/dssp/Q8ZJK9.dssp similarity index 99% rename from toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q8ZJK9.dssp rename to toy_example/data/dssp/Q8ZJK9.dssp index 1108839..83a5704 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q8ZJK9.dssp +++ b/toy_example/data/dssp/Q8ZJK9.dssp @@ -1,4 +1,4 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . +==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2024-03-21 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER 01-JUN-22 . COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q97VM8.dssp b/toy_example/data/dssp/Q97VM8.dssp similarity index 99% rename from toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q97VM8.dssp rename to toy_example/data/dssp/Q97VM8.dssp index 8aec832..aff5d92 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q97VM8.dssp +++ b/toy_example/data/dssp/Q97VM8.dssp @@ -1,4 +1,4 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . +==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2024-03-21 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER 01-JUN-22 . COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/O84332.dssp b/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/O84332.dssp deleted file mode 100644 index d2a24e6..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/O84332.dssp +++ /dev/null @@ -1,302 +0,0 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . -REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . -HEADER 01-JUN-22 . -COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . -SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: CHLAMYDIA TRACHOMATIS (STRAIN D/UW-3/C . -AUTHOR . - 274 1 0 0 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) . - 13288.5 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) . - 196 71.5 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES . - 36 13.1 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES . - 28 10.2 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES . - 31 11.3 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES . - 89 32.5 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES . - 4 1.5 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES . - 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** . - 0 0 0 0 1 3 1 2 0 1 1 0 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 RESIDUES PER ALPHA HELIX . - 2 2 1 3 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PARALLEL BRIDGES PER LADDER . - 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ANTIPARALLEL BRIDGES PER LADDER . - 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LADDERS PER SHEET . - # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA CHAIN - 1 1 A M 0 0 234 0, 0.0 2,-0.5 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 82.9 17.5 18.0 -30.6 - 2 2 A F - 0 0 213 2,-0.0 2,-0.7 0, 0.0 0, 0.0 -0.990 360.0-143.5-109.3 104.4 15.0 16.4 -28.3 - 3 3 A T - 0 0 119 -2,-0.5 2,-0.6 1,-0.1 0, 0.0 -0.750 15.9-122.7 -71.7 115.8 12.0 18.6 -29.0 - 4 4 A D - 0 0 150 -2,-0.7 2,-1.2 1,-0.1 -1,-0.1 -0.484 22.7-160.1 -55.3 98.2 10.1 19.1 -25.8 - 5 5 A K - 0 0 174 -2,-0.6 2,-0.8 2,-0.0 -1,-0.1 -0.838 11.6-147.4 -83.0 90.9 6.6 17.8 -26.7 - 6 6 A E - 0 0 144 -2,-1.2 2,-1.6 1,-0.1 -2,-0.0 -0.517 15.3-138.1 -49.1 99.8 4.7 19.5 -23.9 - 7 7 A T - 0 0 120 -2,-0.8 2,-2.0 1,-0.1 -1,-0.1 -0.664 13.0-151.3 -70.6 90.8 2.1 16.7 -23.5 - 8 8 A H - 0 0 159 -2,-1.6 2,-0.3 3,-0.0 -1,-0.1 -0.555 10.4-163.2 -63.5 81.6 -0.9 19.0 -23.1 - 9 9 A R - 0 0 96 -2,-2.0 70,-0.1 1,-0.1 69,-0.0 -0.601 34.9-104.8 -55.7 123.8 -3.0 16.6 -21.0 - 10 10 A K - 0 0 149 -2,-0.3 2,-2.2 68,-0.3 -1,-0.1 -0.341 51.9 -85.8 -46.3 144.3 -6.5 18.1 -21.3 - 11 11 A P + 0 0 136 0, 0.0 -1,-0.2 0, 0.0 3,-0.1 -0.412 59.3 175.9 -71.3 80.4 -7.1 19.9 -17.9 - 12 12 A F - 0 0 63 -2,-2.2 -3,-0.0 1,-0.1 68,-0.0 -0.600 49.5 -81.2 -68.8 145.4 -8.5 16.9 -15.9 - 13 13 A P - 0 0 52 0, 0.0 -1,-0.1 0, 0.0 2,-0.0 -0.266 46.8-118.5 -55.3 135.0 -9.0 18.1 -12.3 - 14 14 A T > - 0 0 94 1,-0.1 4,-2.4 -3,-0.1 3,-0.2 -0.358 28.5-107.1 -62.3 155.0 -5.8 18.1 -10.2 - 15 15 A W H > S+ 0 0 25 1,-0.2 4,-2.8 2,-0.2 5,-0.3 0.862 123.8 60.6 -53.6 -34.4 -5.8 15.8 -7.1 - 16 16 A A H > S+ 0 0 51 1,-0.2 4,-1.7 2,-0.2 -1,-0.2 0.957 107.4 43.8 -57.1 -48.6 -6.2 19.0 -5.1 - 17 17 A H H > S+ 0 0 108 -3,-0.2 4,-0.6 1,-0.2 -2,-0.2 0.913 115.4 49.3 -62.7 -40.7 -9.5 19.8 -6.9 - 18 18 A L H < S+ 0 0 2 -4,-2.4 3,-0.3 1,-0.2 -2,-0.2 0.898 116.8 39.4 -65.4 -41.7 -10.6 16.1 -6.5 - 19 19 A L H < S+ 0 0 4 -4,-2.8 -1,-0.2 1,-0.2 -2,-0.2 0.601 117.8 48.2 -88.2 -16.2 -9.9 15.8 -2.8 - 20 20 A H H < S+ 0 0 111 -4,-1.7 -1,-0.2 -5,-0.3 -2,-0.2 0.371 96.4 92.4-101.4 -0.3 -11.1 19.4 -1.9 - 21 21 A S S < S- 0 0 32 -4,-0.6 4,-0.2 -3,-0.3 -3,-0.0 -0.557 94.0 -45.9 -90.6 162.5 -14.4 18.9 -3.9 - 22 22 A E > - 0 0 146 -2,-0.2 3,-1.4 1,-0.2 -1,-0.2 0.274 51.5-115.3 -36.8 143.9 -17.7 17.6 -2.4 - 23 23 A P T 3 S+ 0 0 109 0, 0.0 -1,-0.2 0, 0.0 -2,-0.0 0.417 101.6 84.2 -61.4 1.9 -17.7 14.5 -0.0 - 24 24 A S T 3 + 0 0 25 2,-0.1 2,-0.2 249,-0.0 -2,-0.1 0.493 60.3 115.7 -85.5 -8.2 -19.9 12.7 -2.7 - 25 25 A K < - 0 0 25 -3,-1.4 2,-0.5 -4,-0.2 34,-0.2 -0.454 51.7-151.6 -73.2 139.1 -17.0 11.4 -4.9 - 26 26 A Q E -a 59 0A 13 32,-2.7 34,-2.6 -2,-0.2 2,-0.6 -0.913 3.9-153.1-110.5 125.7 -16.3 7.7 -5.2 - 27 27 A F E -ab 60 251A 5 223,-2.6 225,-2.3 -2,-0.5 2,-0.6 -0.877 11.1-174.9-103.4 116.9 -12.8 6.4 -6.0 - 28 28 A V E -ab 61 252A 0 32,-2.5 34,-2.2 -2,-0.6 2,-0.4 -0.896 7.9-179.5-117.7 103.9 -12.5 3.1 -7.8 - 29 29 A F E -ab 62 253A 0 223,-2.8 225,-3.1 -2,-0.6 2,-0.8 -0.887 20.0-145.3-110.2 131.6 -8.9 1.8 -8.2 - 30 30 A G E -ab 63 254A 0 32,-2.7 34,-2.6 -2,-0.4 2,-1.0 -0.823 9.0-161.1 -96.1 103.5 -7.9 -1.4 -9.9 - 31 31 A N E -a 64 0A 7 223,-2.2 227,-0.2 -2,-0.8 228,-0.1 -0.734 8.7-177.5 -81.9 103.3 -4.8 -3.0 -8.3 - 32 32 A W - 0 0 0 32,-1.5 -1,-0.2 -2,-1.0 3,-0.1 0.645 18.7-170.2 -74.5 -13.4 -3.5 -5.4 -10.9 - 33 33 A K - 0 0 42 31,-0.5 2,-1.8 1,-0.2 -1,-0.2 -0.178 64.3 -16.8 52.1-147.5 -0.7 -6.6 -8.5 - 34 34 A M S S+ 0 0 176 31,-0.1 2,-0.3 32,-0.1 -1,-0.2 -0.378 112.2 115.1 -81.3 58.4 1.9 -8.8 -10.2 - 35 35 A N + 0 0 70 -2,-1.8 -3,-0.1 -3,-0.1 -2,-0.0 -0.944 39.7 38.0-131.8 161.4 -0.2 -9.5 -13.3 - 36 36 A K - 0 0 42 -2,-0.3 2,-0.2 29,-0.1 -1,-0.1 0.592 52.4-129.2 75.4 137.0 -0.4 -8.8 -17.1 - 37 37 A T > - 0 0 79 1,-0.0 4,-2.4 32,-0.0 5,-0.2 -0.483 43.9 -93.6 -85.9 171.9 2.2 -8.7 -19.8 - 38 38 A L H > S+ 0 0 82 1,-0.2 4,-2.6 2,-0.2 5,-0.2 0.925 127.4 50.4 -56.2 -45.3 2.4 -5.7 -22.2 - 39 39 A T H > S+ 0 0 96 1,-0.2 4,-2.2 2,-0.2 -1,-0.2 0.892 111.5 47.3 -62.9 -42.2 0.0 -7.4 -24.7 - 40 40 A E H > S+ 0 0 106 2,-0.2 4,-2.5 1,-0.2 -1,-0.2 0.897 112.5 49.8 -68.0 -39.4 -2.6 -8.3 -22.0 - 41 41 A A H X S+ 0 0 2 -4,-2.4 4,-2.9 2,-0.2 -2,-0.2 0.933 111.6 48.1 -65.0 -44.3 -2.4 -4.7 -20.7 - 42 42 A Q H X S+ 0 0 112 -4,-2.6 4,-2.3 2,-0.2 -2,-0.2 0.911 112.5 49.6 -61.3 -42.3 -2.9 -3.2 -24.2 - 43 43 A T H X S+ 0 0 95 -4,-2.2 4,-1.1 -5,-0.2 -2,-0.2 0.937 113.8 46.1 -62.3 -46.5 -5.8 -5.6 -24.8 - 44 44 A F H >X S+ 0 0 9 -4,-2.5 4,-2.3 1,-0.2 3,-0.8 0.965 113.6 47.8 -56.2 -55.8 -7.4 -4.6 -21.5 - 45 45 A L H 3X S+ 0 0 5 -4,-2.9 4,-2.5 1,-0.3 5,-0.3 0.846 104.0 60.2 -64.3 -36.3 -6.9 -0.8 -22.0 - 46 46 A K H 3< S+ 0 0 176 -4,-2.3 4,-0.4 1,-0.2 -1,-0.3 0.857 116.0 33.9 -56.5 -41.6 -8.4 -0.9 -25.6 - 47 47 A S H << S+ 0 0 50 -4,-1.1 -2,-0.2 -3,-0.8 -1,-0.2 0.793 119.9 50.8 -82.2 -33.5 -11.7 -2.2 -24.3 - 48 48 A F H >< S+ 0 0 0 -4,-2.3 3,-1.8 1,-0.2 6,-0.2 0.959 105.3 51.9 -73.1 -50.4 -11.6 -0.3 -20.9 - 49 49 A I T 3< S+ 0 0 54 -4,-2.5 -1,-0.2 1,-0.3 -3,-0.1 0.737 101.2 63.5 -63.7 -26.7 -10.9 3.3 -22.1 - 50 50 A S T 3 S+ 0 0 88 -4,-0.4 2,-0.5 -5,-0.3 -1,-0.3 0.408 76.8 112.3 -77.3 -1.5 -13.8 3.2 -24.6 - 51 51 A S X - 0 0 25 -3,-1.8 3,-1.6 1,-0.1 4,-0.2 -0.690 61.4-148.5 -82.8 123.8 -16.5 2.8 -21.9 - 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249 249 A V < + 0 0 1 -3,-2.1 -19,-0.2 -6,-0.2 3,-0.1 -0.843 42.4 174.1 -94.8 110.0 -16.9 4.4 2.3 - 250 250 A N - 0 0 16 -21,-2.5 -223,-2.6 -2,-0.7 2,-0.3 0.013 61.4 -48.2-102.8 22.2 -15.6 6.8 -0.5 - 251 251 A G E -b 27 0A 0 -22,-0.4 -20,-2.6 -225,-0.3 2,-0.4 -0.892 61.2 -73.3 144.2-165.6 -14.7 4.0 -2.9 - 252 252 A L E -bh 28 231A 0 -225,-2.3 -223,-2.8 -22,-0.3 2,-0.7 -0.987 8.8-152.5-136.8 133.9 -13.0 0.7 -3.6 - 253 253 A L E -b 29 0A 4 -22,-2.5 2,-0.6 -2,-0.4 -223,-0.2 -0.897 34.4-157.9-102.3 99.2 -9.5 -0.8 -4.0 - 254 254 A V E -b 30 0A 1 -225,-3.1 -223,-2.2 -2,-0.7 -20,-0.1 -0.717 16.1-179.8 -93.7 120.0 -10.2 -3.7 -6.3 - 255 255 A G > + 0 0 19 -2,-0.6 3,-2.2 -22,-0.4 4,-0.3 0.710 69.5 0.4 -79.2-116.6 -7.9 -6.7 -6.6 - 256 256 A G G > S+ 0 0 56 1,-0.3 3,-1.6 2,-0.2 4,-0.3 0.760 124.8 62.7 -55.8 -31.4 -8.5 -9.7 -8.9 - 257 257 A A G > S+ 0 0 22 -22,-0.3 3,-1.0 1,-0.3 7,-0.3 0.781 93.9 65.3 -65.6 -22.4 -11.8 -8.3 -10.4 - 258 258 A S G < S+ 0 0 0 -3,-2.2 -1,-0.3 1,-0.2 -2,-0.2 0.558 83.8 76.0 -74.4 -8.5 -9.8 -5.4 -11.8 - 259 259 A L G < S+ 0 0 51 -3,-1.6 2,-0.5 -4,-0.3 -1,-0.2 0.705 90.3 60.6 -77.8 -19.8 -7.9 -7.8 -14.1 - 260 260 A S S <> S- 0 0 42 -3,-1.0 4,-2.3 -4,-0.3 5,-0.2 -0.936 73.8-149.5-106.1 129.8 -11.0 -8.1 -16.5 - 261 261 A S H > S+ 0 0 23 -2,-0.5 4,-2.6 2,-0.2 5,-0.2 0.917 100.3 51.7 -63.1 -40.1 -12.2 -4.9 -18.1 - 262 262 A E H > S+ 0 0 138 2,-0.2 4,-2.7 1,-0.2 5,-0.2 0.964 112.4 43.6 -58.1 -55.3 -15.8 -6.3 -18.1 - 263 263 A N H > S+ 0 0 84 2,-0.2 4,-1.9 1,-0.2 -1,-0.2 0.865 115.2 49.1 -62.6 -39.2 -15.7 -7.1 -14.4 - 264 264 A F H X S+ 0 0 0 -4,-2.3 4,-2.4 -7,-0.3 -1,-0.2 0.934 112.3 47.3 -68.9 -42.4 -14.1 -3.8 -13.4 - 265 265 A L H X S+ 0 0 21 -4,-2.6 4,-2.5 1,-0.2 -2,-0.2 0.895 109.4 55.1 -62.9 -39.4 -16.6 -1.8 -15.5 - 266 266 A S H X S+ 0 0 35 -4,-2.7 4,-0.6 2,-0.2 -1,-0.2 0.881 108.9 47.7 -61.7 -38.0 -19.4 -3.8 -13.9 - 267 267 A I H >X S+ 0 0 1 -4,-1.9 3,-1.3 2,-0.2 4,-0.5 0.951 111.4 50.2 -63.9 -48.1 -18.1 -2.8 -10.4 - 268 268 A I H >< S+ 0 0 1 -4,-2.4 3,-1.1 1,-0.3 -2,-0.2 0.879 107.4 55.0 -58.3 -39.5 -17.9 0.9 -11.5 - 269 269 A Q H 3< S+ 0 0 112 -4,-2.5 -1,-0.3 1,-0.2 -2,-0.2 0.655 103.5 56.2 -66.8 -20.0 -21.5 0.7 -12.8 - 270 270 A Q H << S+ 0 0 77 -3,-1.3 2,-0.4 -4,-0.6 -1,-0.2 0.515 77.5 115.9 -92.2 -8.7 -22.7 -0.5 -9.4 - 271 271 A I << - 0 0 11 -3,-1.1 2,-0.3 -4,-0.5 -30,-0.1 -0.494 65.8-134.4 -63.4 118.7 -21.3 2.5 -7.5 - 272 272 A D - 0 0 45 -2,-0.4 -2,-0.1 -31,-0.2 -1,-0.1 -0.611 19.9-163.3 -72.0 131.3 -24.2 4.5 -6.0 - 273 273 A I 0 0 51 -2,-0.3 -248,-0.1 -214,-0.0 -214,-0.0 -0.997 360.0 360.0-120.0 120.2 -23.7 8.2 -6.7 - 274 274 A P 0 0 147 0, 0.0 -250,-0.0 0, 0.0 -216,-0.0 -0.277 360.0 360.0 -65.1 360.0 -25.8 10.6 -4.5 diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q3ZXC5.dssp b/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q3ZXC5.dssp deleted file mode 100644 index 29cc114..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/dssp/Q3ZXC5.dssp +++ /dev/null @@ -1,281 +0,0 @@ -==== Secondary Structure Definition by the program DSSP, CMBI version 2.0 ==== DATE=2023-12-07 . -REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . -HEADER 01-JUN-22 . -COMPND MOL_ID: 1; MOLECULE: TRIOSEPHOSPHATE ISOMERASE; CHAIN: A . -SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: DEHALOCOCCOIDES MCCARTYI (STRAIN CBDB1 . -AUTHOR . - 253 1 0 0 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) . - 12038.2 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) . - 178 70.4 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES . - 33 13.0 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES . - 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES . - 19 7.5 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES . - 25 9.9 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES . - 91 36.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES . - 3 1.2 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES . - 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** . - 0 0 0 1 2 1 1 0 0 1 0 0 2 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 RESIDUES PER ALPHA HELIX . - 1 2 1 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PARALLEL BRIDGES PER LADDER . - 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ANTIPARALLEL BRIDGES PER LADDER . - 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LADDERS PER SHEET . - # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA CHAIN - 1 1 A M 0 0 155 0, 0.0 2,-0.3 0, 0.0 199,-0.0 0.000 360.0 360.0 360.0 147.2 -5.2 -9.9 14.7 - 2 2 A R - 0 0 51 200,-0.1 2,-0.3 1,-0.1 200,-0.1 -0.625 360.0-109.2 -75.2 142.0 -4.8 -7.4 11.8 - 3 3 A Q - 0 0 98 -2,-0.3 2,-0.3 198,-0.2 33,-0.1 -0.599 29.3-120.7 -71.7 132.0 -2.4 -8.8 9.2 - 4 4 A I - 0 0 12 31,-0.4 33,-2.7 -2,-0.3 2,-0.5 -0.607 29.0-161.2 -72.9 131.2 1.0 -7.0 9.0 - 5 5 A I E -ab 37 226A 4 220,-2.2 222,-2.2 -2,-0.3 2,-0.6 -0.963 11.6-169.3-118.5 125.2 1.6 -5.4 5.5 - 6 6 A I E -ab 38 227A 0 31,-3.1 33,-2.8 -2,-0.5 2,-0.5 -0.935 13.1-177.3-112.3 108.9 5.1 -4.5 4.2 - 7 7 A A E -ab 39 228A 0 220,-2.8 222,-2.9 -2,-0.6 2,-0.8 -0.925 16.5-148.8-109.3 124.5 4.7 -2.4 1.0 - 8 8 A G E -ab 40 229A 0 31,-3.0 33,-2.8 -2,-0.5 2,-0.9 -0.831 7.1-163.1 -92.4 106.2 7.8 -1.2 -0.9 - 9 9 A N E -a 41 0A 7 220,-2.3 224,-0.2 -2,-0.8 225,-0.1 -0.785 7.7-177.5 -86.6 102.8 7.2 2.2 -2.7 - 10 10 A W - 0 0 1 31,-1.7 -1,-0.2 -2,-0.9 3,-0.1 0.660 18.5-169.9 -74.0 -15.3 10.0 2.4 -5.2 - 11 11 A K - 0 0 47 30,-0.5 2,-1.8 1,-0.2 -1,-0.2 -0.178 62.2 -18.0 53.3-150.5 8.9 5.9 -6.4 - 12 12 A M S S+ 0 0 182 30,-0.1 2,-0.3 31,-0.1 -1,-0.2 -0.408 110.0 115.0 -80.8 59.3 10.6 7.2 -9.6 - 13 13 A N + 0 0 76 -2,-1.8 -3,-0.1 -3,-0.1 6,-0.0 -0.919 43.1 37.7-127.1 163.2 13.5 4.7 -9.3 - 14 14 A T - 0 0 32 -2,-0.3 2,-0.1 28,-0.1 32,-0.1 0.670 59.4-122.4 71.9 131.7 14.9 1.8 -11.4 - 15 15 A T > - 0 0 75 1,-0.0 4,-2.8 30,-0.0 5,-0.2 -0.419 46.3 -91.9 -73.5 170.9 15.2 1.1 -15.1 - 16 16 A L H > S+ 0 0 86 1,-0.2 4,-2.2 2,-0.2 5,-0.1 0.899 129.1 45.9 -54.3 -44.2 13.4 -2.0 -16.5 - 17 17 A S H > S+ 0 0 85 2,-0.2 4,-2.7 1,-0.2 5,-0.2 0.919 112.8 48.4 -69.3 -44.6 16.7 -4.1 -16.0 - 18 18 A E H > S+ 0 0 108 2,-0.2 4,-2.7 1,-0.2 -2,-0.2 0.918 112.1 51.0 -61.7 -42.3 17.4 -2.8 -12.5 - 19 19 A A H X S+ 0 0 0 -4,-2.8 4,-2.4 2,-0.2 -2,-0.2 0.931 112.5 45.3 -58.5 -49.8 13.7 -3.5 -11.5 - 20 20 A C H X S+ 0 0 26 -4,-2.2 4,-2.6 -5,-0.2 -2,-0.2 0.944 115.1 47.0 -62.0 -48.6 14.0 -7.1 -12.8 - 21 21 A T H X S+ 0 0 80 -4,-2.7 4,-2.5 2,-0.2 -2,-0.2 0.909 111.7 51.8 -58.9 -44.8 17.4 -7.8 -11.2 - 22 22 A L H X S+ 0 0 20 -4,-2.7 4,-1.1 -5,-0.2 -2,-0.2 0.953 112.5 43.8 -61.1 -50.4 16.1 -6.3 -7.9 - 23 23 A V H >X S+ 0 0 0 -4,-2.4 4,-2.2 1,-0.2 3,-0.8 0.930 113.9 51.1 -60.9 -45.8 13.0 -8.5 -7.7 - 24 24 A Q H 3X S+ 0 0 119 -4,-2.6 4,-0.6 1,-0.2 -1,-0.2 0.896 106.6 55.2 -58.5 -40.4 15.0 -11.6 -8.8 - 25 25 A S H 3< S+ 0 0 72 -4,-2.5 -1,-0.2 1,-0.2 -2,-0.2 0.743 120.2 29.6 -66.8 -24.8 17.6 -11.0 -6.0 - 26 26 A M H < S+ 0 0 0 -4,-2.7 3,-1.3 1,-0.2 -2,-0.2 0.857 105.5 58.0 -66.2 -35.5 10.7 -13.1 0.4 - 31 31 A E H 3< S+ 0 0 57 -4,-2.4 -1,-0.2 -5,-0.3 -2,-0.2 0.845 101.3 56.5 -62.3 -32.6 8.9 -16.4 -0.6 - 32 32 A R T 3< S+ 0 0 173 -4,-1.0 2,-0.8 -3,-0.2 -1,-0.2 0.526 88.7 90.3 -74.2 -10.2 10.3 -18.1 2.6 - 33 33 A I < + 0 0 11 -3,-1.3 3,-0.2 -4,-0.3 2,-0.1 -0.831 60.6 179.8 -94.8 108.7 8.7 -15.3 4.8 - 34 34 A E + 0 0 157 -2,-0.8 3,-0.1 1,-0.1 -2,-0.0 -0.450 50.1 44.6 -99.9 171.2 5.2 -16.4 5.9 - 35 35 A G S S+ 0 0 44 -2,-0.1 -31,-0.4 1,-0.1 2,-0.3 0.062 98.3 75.6 85.9 -20.9 2.5 -14.7 8.0 - 36 36 A I S S- 0 0 11 -3,-0.2 2,-0.4 -33,-0.1 -31,-0.2 -0.810 79.2-114.7-118.7 159.4 2.7 -11.2 6.5 - 37 37 A E E -a 5 0A 26 -33,-2.7 -31,-3.1 -2,-0.3 2,-0.5 -0.801 27.4-161.6 -91.8 131.2 1.7 -9.5 3.2 - 38 38 A K E -a 6 0A 6 -2,-0.4 22,-3.1 20,-0.4 2,-0.4 -0.971 10.4-178.2-118.8 118.9 4.6 -8.3 1.0 - 39 39 A I E -ac 7 60A 0 -33,-2.8 -31,-3.0 -2,-0.5 2,-0.4 -0.958 12.3-162.3-122.5 134.3 3.8 -5.7 -1.7 - 40 40 A I E -ac 8 61A 0 20,-2.3 22,-2.6 -2,-0.4 -31,-0.2 -0.976 2.1-167.2-113.7 131.4 6.2 -4.2 -4.3 - 41 41 A C E +a 9 0A 0 -33,-2.8 -31,-1.7 -2,-0.4 -30,-0.5 -0.781 17.8 171.9-118.9 82.5 5.2 -0.9 -6.0 - 42 42 A P - 0 0 0 0, 0.0 22,-0.4 0, 0.0 -28,-0.1 -0.319 44.4 -77.0 -79.7 169.5 7.5 -0.3 -9.0 - 43 43 A P >> - 0 0 22 0, 0.0 3,-2.1 0, 0.0 4,-0.6 -0.328 51.4-103.3 -57.3 154.1 7.1 2.4 -11.7 - 44 44 A F H >> S+ 0 0 74 1,-0.3 3,-1.3 2,-0.2 4,-0.5 0.828 119.4 61.5 -52.5 -40.1 4.4 1.6 -14.4 - 45 45 A I H 34 S+ 0 0 121 1,-0.3 -1,-0.3 2,-0.1 3,-0.1 0.720 107.5 45.8 -59.4 -23.8 7.0 0.6 -17.0 - 46 46 A S H <> S+ 0 0 0 -3,-2.1 4,-2.1 1,-0.1 -1,-0.3 0.494 87.4 89.0-101.1 -6.6 8.2 -2.3 -14.7 - 47 47 A L H S+ 0 0 28 0, 0.0 4,-2.3 0, 0.0 -1,-0.2 0.886 115.7 52.0 -66.8 -33.7 7.9 -7.8 -16.4 - 50 50 A I H X S+ 0 0 0 -4,-2.1 4,-2.4 2,-0.2 -2,-0.2 0.923 106.2 54.9 -65.1 -40.2 7.7 -7.8 -12.6 - 51 51 A K H < S+ 0 0 86 -4,-2.6 4,-0.2 -5,-0.2 -1,-0.2 0.931 109.3 47.6 -54.4 -47.1 4.3 -9.6 -12.8 - 52 52 A T H >< S+ 0 0 64 -4,-2.0 3,-1.3 1,-0.2 -2,-0.2 0.916 112.3 48.6 -61.3 -43.6 6.0 -12.3 -15.0 - 53 53 A I H 3< S+ 0 0 30 -4,-2.3 -1,-0.2 1,-0.2 -2,-0.2 0.860 110.7 52.7 -63.3 -35.5 8.9 -12.6 -12.5 - 54 54 A L T >< S+ 0 0 14 -4,-2.4 3,-2.1 -5,-0.1 -1,-0.2 0.320 76.4 137.3 -87.4 7.8 6.3 -12.9 -9.6 - 55 55 A E T < S+ 0 0 113 -3,-1.3 3,-0.1 1,-0.3 -3,-0.1 -0.307 80.9 6.3 -53.9 134.4 4.3 -15.7 -11.3 - 56 56 A N T 3 S+ 0 0 167 1,-0.2 2,-0.3 2,-0.0 -1,-0.3 0.679 105.4 132.0 56.3 24.6 3.4 -18.3 -8.6 - 57 57 A S < - 0 0 20 -3,-2.1 -1,-0.2 2,-0.2 -3,-0.1 -0.773 63.5-139.2 -97.4 148.5 4.9 -16.0 -5.8 - 58 58 A S S S+ 0 0 49 -2,-0.3 -20,-0.4 -3,-0.1 2,-0.2 0.683 78.7 104.2 -68.3 -22.0 3.4 -15.0 -2.5 - 59 59 A I - 0 0 7 -22,-0.1 2,-0.2 -32,-0.1 -2,-0.2 -0.472 66.8-142.5 -67.5 129.7 4.7 -11.5 -3.2 - 60 60 A K E -c 39 0A 78 -22,-3.1 -20,-2.3 -2,-0.2 2,-0.4 -0.610 4.6-134.4 -93.7 154.3 2.0 -9.0 -4.3 - 61 61 A L E -c 40 0A 5 -2,-0.2 27,-2.3 -22,-0.2 28,-2.0 -0.875 22.8-178.8-110.2 140.3 2.3 -6.3 -7.0 - 62 62 A G E -d 89 0A 0 -22,-2.6 28,-0.3 -2,-0.4 2,-0.2 -0.958 21.7-128.7-133.1 153.2 1.0 -2.7 -6.6 - 63 63 A A E -d 90 0A 0 26,-2.5 28,-2.7 -2,-0.3 3,-0.1 -0.664 15.0-135.6 -91.2 158.6 0.9 0.5 -8.7 - 64 64 A Q S S- 0 0 35 -22,-0.4 2,-0.3 -2,-0.2 30,-0.2 0.544 82.0 -11.9 -88.9 -11.8 2.2 3.9 -7.4 - 65 65 A N - 0 0 7 27,-0.1 2,-0.3 28,-0.1 -1,-0.2 -0.955 57.5-160.2-167.5 168.0 -0.9 5.8 -8.8 - 66 66 A L - 0 0 0 -2,-0.3 2,-0.3 25,-0.1 13,-0.2 -0.968 23.1-117.7-148.3 164.6 -4.0 5.5 -11.1 - 67 67 A F - 0 0 23 11,-2.8 -2,-0.0 -2,-0.3 7,-0.0 -0.765 24.9-128.1 -94.5 149.4 -6.4 7.9 -12.9 - 68 68 A Y S S+ 0 0 70 -2,-0.3 2,-0.4 11,-0.1 11,-0.1 0.478 83.4 83.5 -82.7 -2.4 -10.1 7.7 -11.8 - 69 69 A Q S S- 0 0 80 1,-0.1 -2,-0.2 9,-0.1 12,-0.2 -0.831 71.0-142.3 -99.6 143.4 -11.5 7.2 -15.4 - 70 70 A E S S- 0 0 87 -2,-0.4 2,-0.3 1,-0.2 11,-0.2 0.832 81.2 -20.8 -67.9 -35.6 -11.7 3.8 -17.1 - 71 71 A K S S+ 0 0 172 7,-0.1 2,-0.3 10,-0.1 -1,-0.2 -0.962 80.9 105.3-164.8 161.0 -10.7 5.3 -20.5 - 72 72 A G S S- 0 0 58 -2,-0.3 2,-2.0 -3,-0.1 -3,-0.0 -0.934 76.0 -35.4 153.3-170.1 -10.6 8.6 -22.5 - 73 73 A A S S+ 0 0 102 -2,-0.3 2,-0.3 1,-0.1 -2,-0.0 -0.459 81.2 127.2 -79.2 64.6 -8.6 11.5 -23.8 - 74 74 A Y > - 0 0 99 -2,-2.0 3,-2.3 3,-0.1 -1,-0.1 -0.639 47.8-158.0-122.2 63.5 -6.1 11.5 -20.8 - 75 75 A T T 3 S+ 0 0 152 -2,-0.3 3,-0.1 1,-0.3 -2,-0.1 -0.299 77.7 13.4 -52.8 121.4 -2.7 11.2 -22.6 - 76 76 A G T 3 S+ 0 0 71 1,-0.3 -1,-0.3 -2,-0.1 2,-0.2 0.107 98.8 121.0 96.3 -14.6 -0.1 9.8 -20.1 - 77 77 A E < - 0 0 78 -3,-2.3 2,-0.5 -11,-0.0 -1,-0.3 -0.467 55.3-139.0 -81.2 151.2 -2.7 8.6 -17.5 - 78 78 A I - 0 0 43 -2,-0.2 -11,-2.8 -3,-0.1 -9,-0.1 -0.941 19.7-142.8-111.2 123.2 -3.0 4.9 -16.4 - 79 79 A S > - 0 0 8 -2,-0.5 4,-1.7 -13,-0.2 3,-0.3 -0.407 21.3-117.4 -82.3 161.2 -6.6 3.6 -15.9 - 80 80 A P H > S+ 0 0 3 0, 0.0 4,-2.3 0, 0.0 -10,-0.1 0.859 116.7 58.0 -61.8 -33.5 -7.9 1.2 -13.2 - 81 81 A L H 4 S+ 0 0 67 1,-0.2 4,-0.4 2,-0.2 -11,-0.1 0.844 105.8 48.1 -68.2 -34.2 -8.8 -1.3 -16.1 - 82 82 A M H >4 S+ 0 0 104 -3,-0.3 3,-0.5 -12,-0.2 4,-0.2 0.879 114.2 47.6 -68.8 -39.3 -5.1 -1.3 -17.3 - 83 83 A L H >X S+ 0 0 1 -4,-1.7 4,-2.8 1,-0.2 3,-2.2 0.868 97.1 67.0 -75.3 -37.0 -3.9 -1.9 -13.7 - 84 84 A K T 3< S+ 0 0 114 -4,-2.3 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1,-0.2 -2,-0.2 0.887 108.3 55.1 -65.9 -36.9 -2.2 6.0 13.8 - 184 184 A G H X S+ 0 0 22 -4,-2.4 4,-1.6 -5,-0.2 -1,-0.2 0.892 108.9 48.8 -60.4 -37.4 -4.5 5.4 16.8 - 185 185 A Y H X S+ 0 0 38 -4,-1.8 4,-2.4 2,-0.2 -2,-0.2 0.937 108.9 51.8 -67.7 -44.0 -6.3 8.7 15.9 - 186 186 A I H X S+ 0 0 0 -4,-2.4 4,-2.5 1,-0.2 -2,-0.2 0.923 107.8 53.8 -55.2 -44.8 -6.6 7.5 12.2 - 187 187 A R H X S+ 0 0 18 -4,-2.5 4,-1.8 2,-0.2 -1,-0.2 0.879 108.4 49.1 -59.4 -40.7 -8.2 4.3 13.5 - 188 188 A R H X S+ 0 0 165 -4,-1.6 4,-2.4 2,-0.2 -2,-0.2 0.951 110.1 50.2 -61.9 -49.4 -10.7 6.3 15.5 - 189 189 A V H X S+ 0 0 2 -4,-2.4 4,-1.9 1,-0.2 5,-0.2 0.874 108.8 53.0 -60.6 -38.0 -11.6 8.5 12.4 - 190 190 A L H X>S+ 0 0 0 -4,-2.5 4,-3.0 2,-0.2 5,-0.5 0.912 110.2 48.3 -59.5 -43.4 -12.1 5.3 10.4 - 191 191 A G H X5S+ 0 0 18 -4,-1.8 4,-1.1 1,-0.2 -2,-0.2 0.906 113.4 46.5 -62.3 -42.5 -14.5 4.0 13.1 - 192 192 A D H <5S+ 0 0 113 -4,-2.4 -1,-0.2 2,-0.1 -2,-0.2 0.790 123.0 35.1 -69.6 -30.3 -16.4 7.3 13.1 - 193 193 A T H <5S+ 0 0 48 -4,-1.9 -2,-0.2 -5,-0.2 -3,-0.2 0.865 135.2 17.2 -94.3 -43.7 -16.6 7.4 9.2 - 194 194 A L H <5S- 0 0 21 -4,-3.0 4,-0.4 1,-0.2 -3,-0.2 0.391 111.6-105.3-114.0 -3.6 -17.0 3.8 8.1 - 195 195 A G X< - 0 0 30 -4,-1.1 4,-1.5 -5,-0.5 3,-0.4 -0.074 43.8 -61.7 92.8 167.2 -18.1 2.1 11.4 - 196 196 A N H > S+ 0 0 115 1,-0.2 4,-1.8 2,-0.2 5,-0.2 0.809 126.6 62.0 -59.9 -33.6 -16.5 -0.1 14.0 - 197 197 A A H >> S+ 0 0 59 1,-0.2 4,-2.2 2,-0.2 3,-0.6 0.971 105.3 47.8 -55.8 -50.7 -15.8 -3.0 11.6 - 198 198 A A H 3> S+ 0 0 0 -3,-0.4 4,-2.2 -4,-0.4 -40,-0.3 0.872 109.5 53.1 -59.0 -41.1 -13.5 -0.7 9.5 - 199 199 A A H 3< S+ 0 0 7 -4,-1.5 -1,-0.3 1,-0.2 -2,-0.2 0.852 115.4 40.8 -61.0 -36.1 -11.7 0.5 12.6 - 200 200 A Q H << S+ 0 0 102 -4,-1.8 -2,-0.2 -3,-0.6 -1,-0.2 0.811 124.6 32.3 -84.7 -32.4 -10.9 -3.1 13.7 - 201 201 A T H < S+ 0 0 71 -4,-2.2 -198,-0.2 -45,-0.3 -3,-0.2 0.687 90.1 101.2-104.4 -21.4 -10.0 -4.7 10.3 - 202 202 A S < - 0 0 0 -4,-2.2 2,-0.3 -5,-0.3 -43,-0.2 -0.520 69.0-133.0 -68.4 121.9 -8.4 -1.9 8.4 - 203 203 A P - 0 0 10 0, 0.0 -43,-2.3 0, 0.0 2,-0.5 -0.588 16.3-158.5 -69.4 132.3 -4.5 -2.1 8.3 - 204 204 A I E -g 160 0A 0 -2,-0.3 21,-2.6 19,-0.3 22,-0.3 -0.955 11.7-160.3-117.7 112.1 -2.8 1.2 9.1 - 205 205 A L E -g 161 0A 0 -45,-3.2 -43,-2.9 -2,-0.5 2,-0.6 -0.615 19.0-122.5 -91.1 147.2 0.8 1.4 7.9 - 206 206 A Y E -gh 162 227A 0 20,-2.5 22,-2.2 -2,-0.3 -43,-0.2 -0.806 25.2-177.5 -86.5 121.3 3.6 3.7 9.0 - 207 207 A G + 0 0 10 -45,-3.3 -44,-0.2 -2,-0.6 -1,-0.1 0.170 48.2 101.3-105.7 11.2 4.9 5.6 5.9 - 208 208 A G S S- 0 0 5 -46,-0.3 2,-1.0 1,-0.2 22,-0.4 0.024 94.6 -42.0 -76.4-164.9 7.7 7.5 7.6 - 209 209 A S S S+ 0 0 46 -42,-0.3 2,-0.4 -37,-0.2 -1,-0.2 -0.503 71.5 177.6 -68.8 101.4 11.4 6.7 7.5 - 210 210 A V + 0 0 9 -2,-1.0 22,-0.4 18,-0.2 2,-0.3 -0.889 8.4 149.7-108.7 136.8 11.5 2.9 7.9 - 211 211 A N >> - 0 0 46 -2,-0.4 4,-1.9 20,-0.1 3,-0.9 -0.912 61.2 -83.2-149.2 178.2 14.6 0.6 7.8 - 212 212 A E T 34 S+ 0 0 63 -2,-0.3 4,-0.2 1,-0.2 -2,-0.0 0.619 122.5 56.5 -61.7 -14.8 16.0 -2.7 9.2 - 213 213 A K T 34 S+ 0 0 180 2,-0.1 -1,-0.2 1,-0.1 4,-0.2 0.736 117.8 26.7 -89.9 -27.4 17.0 -0.9 12.5 - 214 214 A N T <> S+ 0 0 26 -3,-0.9 4,-2.3 2,-0.1 3,-0.3 0.573 93.0 90.0-115.0 -13.7 13.7 0.6 13.5 - 215 215 A I H X S+ 0 0 0 -4,-1.9 4,-2.8 1,-0.2 5,-0.2 0.868 87.7 53.8 -56.4 -40.5 11.0 -1.7 12.0 - 216 216 A T H > S+ 0 0 54 -4,-0.2 4,-1.0 2,-0.2 -1,-0.2 0.910 111.5 44.6 -62.2 -43.2 10.8 -3.9 15.1 - 217 217 A E H 4 S+ 0 0 119 -3,-0.3 3,-0.3 2,-0.2 -2,-0.2 0.919 114.8 48.9 -67.3 -43.1 10.2 -0.9 17.4 - 218 218 A I H >< S+ 0 0 5 -4,-2.3 3,-1.4 1,-0.2 6,-0.2 0.935 113.3 46.0 -61.4 -48.8 7.6 0.6 15.1 - 219 219 A L H 3< S+ 0 0 7 -4,-2.8 -1,-0.2 1,-0.3 -2,-0.2 0.631 98.0 71.3 -76.5 -12.4 5.7 -2.8 14.7 - 220 220 A S T 3< S+ 0 0 66 -4,-1.0 -1,-0.3 -3,-0.3 2,-0.3 0.503 79.5 104.5 -74.6 -5.5 5.8 -3.4 18.4 - 221 221 A Q S X S- 0 0 50 -3,-1.4 3,-0.9 -4,-0.2 -44,-0.0 -0.597 78.9-127.0 -80.7 142.9 3.2 -0.6 18.7 - 222 222 A T T 3 S+ 0 0 107 -2,-0.3 -1,-0.1 1,-0.3 -3,-0.0 0.713 103.6 36.3 -65.3 -28.6 -0.5 -1.5 19.3 - 223 223 A N T 3 S+ 0 0 39 -20,-0.0 2,-0.6 2,-0.0 -19,-0.3 0.506 91.4 99.3-102.3 -8.1 -2.0 0.4 16.4 - 224 224 A I < + 0 0 6 -3,-0.9 -19,-0.2 -6,-0.2 -3,-0.1 -0.761 41.1 177.9 -93.9 117.8 0.7 -0.1 13.7 - 225 225 A D - 0 0 9 -21,-2.6 -220,-2.2 -2,-0.6 2,-0.3 0.003 59.7 -50.5-106.9 22.0 -0.2 -2.8 11.2 - 226 226 A G E -b 5 0A 0 -22,-0.3 -20,-2.5 -222,-0.3 2,-0.3 -0.944 61.4 -77.9 144.3-163.7 2.8 -2.5 8.9 - 227 227 A A E -bh 6 206A 0 -222,-2.2 -220,-2.8 -2,-0.3 2,-0.8 -1.000 7.0-145.7-144.6 141.9 4.9 -0.1 6.8 - 228 228 A L E -b 7 0A 6 -22,-2.2 2,-0.5 -2,-0.3 -220,-0.2 -0.888 39.4-155.9-100.1 95.2 5.0 1.8 3.5 - 229 229 A V E -b 8 0A 0 -222,-2.9 -220,-2.3 -2,-0.8 -20,-0.1 -0.664 17.1-178.3 -87.3 121.1 8.8 1.6 2.9 - 230 230 A G S > S- 0 0 18 -2,-0.5 3,-2.3 -22,-0.4 4,-0.3 0.690 70.0 -0.3 -79.7-116.3 10.5 4.2 0.7 - 231 231 A G G > S+ 0 0 54 1,-0.3 3,-1.4 2,-0.2 4,-0.1 0.734 123.8 64.5 -57.8 -28.2 14.3 4.0 -0.1 - 232 232 A A G > S+ 0 0 16 -22,-0.4 3,-1.1 1,-0.2 7,-0.5 0.756 93.1 65.1 -66.9 -20.0 15.0 0.8 2.0 - 233 233 A S G < S+ 0 0 0 -3,-2.3 -1,-0.2 1,-0.2 -2,-0.2 0.630 90.5 65.4 -74.5 -12.6 12.7 -1.1 -0.5 - 234 234 A L G < S+ 0 0 47 -3,-1.4 2,-0.5 -4,-0.3 -1,-0.2 0.390 92.1 71.7 -86.7 -1.2 15.3 -0.4 -3.3 - 235 235 A K S <> S- 0 0 137 -3,-1.1 4,-2.8 1,-0.2 5,-0.3 -0.969 72.8-151.8-120.1 114.1 17.9 -2.6 -1.4 - 236 236 A A H > S+ 0 0 22 -2,-0.5 4,-2.7 1,-0.2 5,-0.2 0.900 95.7 46.7 -51.5 -51.3 17.1 -6.4 -1.6 - 237 237 A E H > S+ 0 0 174 1,-0.2 4,-2.4 2,-0.2 -1,-0.2 0.907 114.7 46.9 -61.6 -44.4 18.9 -7.2 1.8 - 238 238 A S H > S+ 0 0 17 2,-0.2 4,-2.7 1,-0.2 -2,-0.2 0.947 114.5 46.0 -62.6 -49.2 17.2 -4.3 3.6 - 239 239 A F H X S+ 0 0 0 -4,-2.8 4,-2.5 -7,-0.5 -2,-0.2 0.917 114.2 48.0 -65.2 -41.3 13.7 -5.0 2.3 - 240 240 A V H X S+ 0 0 10 -4,-2.7 4,-2.6 -5,-0.3 -1,-0.2 0.913 112.2 50.5 -61.0 -44.1 14.1 -8.8 3.0 - 241 241 A S H X S+ 0 0 33 -4,-2.4 4,-2.6 -5,-0.2 5,-0.2 0.929 110.2 49.3 -61.5 -44.5 15.3 -7.9 6.6 - 242 242 A I H X S+ 0 0 0 -4,-2.7 4,-2.5 1,-0.2 -2,-0.2 0.943 113.4 46.7 -58.2 -49.8 12.3 -5.6 7.2 - 243 243 A C H X S+ 0 0 0 -4,-2.5 4,-2.4 2,-0.2 -2,-0.2 0.903 112.6 50.0 -60.4 -42.5 9.9 -8.4 6.0 - 244 244 A R H X S+ 0 0 113 -4,-2.6 4,-1.7 2,-0.2 -2,-0.2 0.925 112.7 45.8 -65.2 -44.6 11.6 -11.0 8.2 - 245 245 A Q H X S+ 0 0 46 -4,-2.6 4,-1.6 2,-0.2 -2,-0.2 0.908 111.4 53.2 -64.5 -40.8 11.5 -8.8 11.3 - 246 246 A A H X S+ 0 0 0 -4,-2.5 4,-2.5 -5,-0.2 -2,-0.2 0.917 107.3 51.3 -60.1 -43.0 7.8 -8.0 10.6 - 247 247 A A H X S+ 0 0 9 -4,-2.4 4,-1.7 1,-0.2 -1,-0.2 0.868 105.5 55.8 -64.3 -35.2 7.0 -11.7 10.3 - 248 248 A V H < S+ 0 0 81 -4,-1.7 4,-0.3 2,-0.2 -1,-0.2 0.885 110.5 45.8 -62.6 -38.2 8.7 -12.3 13.8 - 249 249 A I H >< S+ 0 0 8 -4,-1.6 3,-1.4 1,-0.2 4,-0.3 0.929 108.7 55.4 -70.0 -43.7 6.4 -9.6 15.3 - 250 250 A Q H >< S+ 0 0 24 -4,-2.5 3,-0.8 1,-0.3 -2,-0.2 0.845 107.7 49.9 -54.5 -39.7 3.2 -11.1 13.5 - 251 251 A N T 3< S+ 0 0 120 -4,-1.7 -1,-0.3 1,-0.2 -2,-0.2 0.480 96.9 68.7 -83.2 -7.2 3.9 -14.5 15.1 - 252 252 A K T < 0 0 142 -3,-1.4 -1,-0.2 -4,-0.3 -2,-0.2 0.530 360.0 360.0 -81.6 -9.2 4.3 -13.2 18.7 - 253 253 A H < 0 0 161 -3,-0.8 -2,-0.2 -4,-0.3 -3,-0.1 0.575 360.0 360.0-135.3 360.0 0.6 -12.3 18.9 diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/dssp_merged_finalMSA_alignment.fasta b/toy_example/results/toy_example_2023_12_07_20_58_09/msas/dssp_merged_finalMSA_alignment.fasta deleted file mode 100644 index 81b97a2..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/dssp_merged_finalMSA_alignment.fasta +++ /dev/null @@ -1,22 +0,0 @@ ->P72484 ----------------------XXXXXEEEEEXX-----SXXXHHHHHHHHHHHTTSS-X--XTTTXEEEEEEXGGGHHHHHHHTT--TSSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHTXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHHHXEEEEXXGGGT-TSSXXXXHHHHHHHHHHHHHHHHHHHXHHHHHHSEEEEXSSXXTTTHHHHHTSSSXXEEEESGGGSSHHHHHHTTGG-GX------------ ->A5FRB6 -----------------------XXXXEEEEEXX-----SXXXHHHHHHHHHHHHHHH-H--TXXSSEEEEEXXHHHHHHHHHHTT--TXSXEEEESXXXSSSSSSXTTXXXHHHHTTT-XSEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHTTXX--X-SXXEEEEXXGGGT-TSSXXXXHHHHHHHHHHHHHHHHHHHXHHHHHHSXEEEXSSXXTTTHHHHHTSTTXXEEEEXGGGGSHHHHHHHHHHHHHHH-TTX------ ->A0QHY3 ----------------------XXXXXEEEEEXX-----SXXXHHHHHHHHHHHHHHS-XGGGGGTXEEEEEXXGGGHHHHHHHHHHHTXSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHTTXEEEEXXGGGS-SSSXXXXHHHHHHHHHHHHHHHHHHSXHHHHTTSEEEEXSXXXTTTHHHHHTSTTXXEEEEXGGGGSHHHHHHHHHHHTTXX-X-X------ ->P9WG42 ----------------------XXXXXEEEEEXX-----SXXXHHHHHHHHHHHHHHS-XGGGGGTXEEEEEXXGGGHHHHHHHHHHHTXSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHTTXEEEEXXGGGT-TSSXXXXHHHHHHHHHHHHHHHHHHTXHHHHTTSEEEEXSXXXTTTHHHHHTSTTXXEEEEXGGGGSHHHHHHHHHHHTTSS-X-X------ ->Q3KM32 -XXXXXXXXXXXXXXHHHHHTSXTTXEEEEEEXX-----SXXXHHHHHHHHHHHTTXGGG--GXTTEEEEEEXXGGGHHHHHHHHT--TSSXEEEESXXBSSSSSSXTTXXBHHHHHHHTXXEEEESXHHHHHTSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTSXTTX--XXEEEEXXGGGS-SSSXXXXHHHHHHHHHHHHHHHHHHSXHHHHHHSXEEEXSXXXHHHHHHHHTSTTXXEEEESGGGGSHHHHHHHHHHSXXX----------- ->A0R756 -------------XXXTTX-X-XSXXEEEEEEXT-----TXXXHHHHHHHHHHHHHHH-HHSXXTTEEEEEEXXGGGHHHHHHHHXT-TXSSEEEESXXBSSSSSSXTTXXBHHHHHHTTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHTTXXHHHHTTXEEEEXXGGGSSTTXXXXXHHHHHHHHHHHIIIII-----TT--SSEEEEEESXXTTTHHHHHHSTTXXEEEESHHHHSHHHHHHHHHHHHHSGGGGX------ ->Q8Z2Y2 -----------------------XXXXEEEEEXX-----SXXXHHHHHHHHHHHHHHT-T--TXXSSEEEEEXXGGGHHHHHHHHT--TSXEEEEESXXXSXSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHHHHXGGGGTTXEEEEXXGGGS-SSSXXXXHHHHHHHHHHHHHHHHTT-XHHHHHHXEEEEXSXXXTTTHHHHHTSTTXXEEEESGGGGSHHHHHHHHHHHHHHH-H-X------ ->Q8ZJK9 -----------------------XXXXEEEEEXX-----SXXXHHHHHHHHHHHHHHH-T--TXXSSEEEEEXXGGGHHHHHHHTT--TSSEEEEESXXXSXSSSSXTTXXXHHHHHHHTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHHTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHHHHXGGGGTTXEEEEXXGGGS-SSSXXXXHHHHHHHHHHHHHHHHTT-XHHHHHHXEEEEXSXXXTTTHHHHHTSTTXXEEEESGGGGSHHHHHHHHHHHHHHT-T-X------ ->A1RUV7 -----------------------XXSSEEEEEXTTXGGGSTHHHHHHHHHHHHHHHHH-------TXEEEEEXXTTTHHHHHTTXS-----SXBEESXXSBSSXSSXTTXXBHHHHHHTTXXEEEESXTTSXXXHHHHHHHHHH----HHHTTXEEEEEESSHHHH--------------------HHHHTTXXSEEEEXXGGGT-TSSXXHHHHXHHHHHHHHHHHHH------HXTTSEEEEESSXXSHHHHHHHHHTTXSEEEEXHHHHTXSSHHHHHHHHHTHH-HHTTSX--X ->Q97VM8 -----------------------XXSSEEEEEXTTXTTSSHHHHHHHHHHHHHHHHHH-------TXXEEEEEXGGGHHHHHHHXS-----SXEEESXXXXXXSSSXTTXXXHHHHHHTTXSEEEESXTTSXXXHHHHHHHHHH----HHHTTXEEEEEESSGGGH--------------------HHHHTTXXSEEEEXXGGGT-TSSXXHHHHXHHHHHHHHHHHTT-------SSSXEEEEXSSXXSHHHHHHHHHTTXSEEEESHHHHTXSSHHHHHHHHHHHH-HHHHXX--- ->Q4JCD8 -----------------------XXSSEEEEEXXSXGGGSHHHHHHHHHHHHHHHHHT-------TXXEEEEEXGGGHHHHHHHXX-----SEEEESXXXXSXSSSXTTXXXHHHHHHTTXXEEEESXTTSXXXHHHHHHHHHH----HHHTTXEEEEEESSGGGH--------------------HHHHTTXXSEEEEXXGGGT-TSSXXHHHHXHHHHHHHHHHHTT-------SSSXEEEEXSSXXSHHHHHHHHHTTXSEEEESHHHHTXSXHHHHHHHHHHHH-HHHHHHHTX diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/dssp_squeezed_merged_finalMSA_alignment.fasta b/toy_example/results/toy_example_2023_12_07_20_58_09/msas/dssp_squeezed_merged_finalMSA_alignment.fasta deleted file mode 100644 index 00ab237..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/dssp_squeezed_merged_finalMSA_alignment.fasta +++ /dev/null @@ -1,22 +0,0 @@ ->P72484 ----------------------XXXXXEEEEEXXS-----XXXHHHHHHHHHHHTTSSXX--TTTXEEEEEEXGGGHHHHHHHTTT--SSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHTXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHHHXEEEEXXGGGTTS-SXXXXHHHHHHHHHHHHHHHHHHHXHHHHHHSEEEEXSSXXTTTHHHHHTSSSXXEEEESGGGSSHHHHHHTTGGGX------------ ->A5FRB6 -----------------------XXXXEEEEEXXS-----XXXHHHHHHHHHHHHHHHHT--XXSSEEEEEXXHHHHHHHHHHTTT--XSXEEEESXXXSSSSSSXTTXXXHHHHTTT-XSEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHH---HHHHHTTXXXSXXEEEEXXGGGTTS-SXXXXHHHHHHHHHHHHHHHHHHHXHHHHHHSXEEEXSSXXTTTHHHHHTSTTXXEEEEXGGGGSHHHHHHHHHHHHHHHTTX------ ->A0QHY3 ----------------------XXXXXEEEEEXXS-----XXXHHHHHHHHHHHHHHSXGGGGGTXEEEEEXXGGGHHHHHHHHHHHTXSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHTTXEEEEXXGGGSSS-SXXXXHHHHHHHHHHHHHHHHHHSXHHHHTTSEEEEXSXXXTTTHHHHHTSTTXXEEEEXGGGGSHHHHHHHHHHHTTXXXX------- ->P9WG42 ----------------------XXXXXEEEEEXXS-----XXXHHHHHHHHHHHHHHSXGGGGGTXEEEEEXXGGGHHHHHHHHHHHTXSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHTTXEEEEXXGGGTTS-SXXXXHHHHHHHHHHHHHHHHHHTXHHHHTTSEEEEXSXXXTTTHHHHHTSTTXXEEEEXGGGGSHHHHHHHHHHHTTSSXX------- ->Q3KM32 -XXXXXXXXXXXXXXHHHHHTSXTTXEEEEEEXXS-----XXXHHHHHHHHHHHTTXGGGG-XTTEEEEEEXXGGGHHHHHHHHTT--SSXEEEESXXBSSSSSSXTTXXBHHHHHHHTXXEEEESXHHHHHTSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHH--HHHHTTTSXTTXXXEEEEXXGGGSSS-SXXXXHHHHHHHHHHHHHHHHHHSXHHHHHHSXEEEXSXXXHHHHHHHHTSTTXXEEEESGGGGSHHHHHHHHHHSXXX---------- ->A0R756 ---------------XXXTTXXXSXXEEEEEEXTT-----XXXHHHHHHHHHHHHHHHHHSXXTTEEEEEEXXGGGHHHHHHHHXT-TXSSEEEESXXBSSSSSSXTTXXBHHHHHHTTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHTTXXHHHHTTXEEEEXXGGGSSTTXXXXXHHHHHHHHHHHIIIIIT-------TSSEEEEEESXXTTTHHHHHHSTTXXEEEESHHHHSHHHHHHHHHHHHHSGGGGX----- ->Q8Z2Y2 -----------------------XXXXEEEEEXXS-----XXXHHHHHHHHHHHHHHTTT--XXSSEEEEEXXGGGHHHHHHHHTT--SXEEEEESXXXSXSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHHHHXGGGGTTXEEEEXXGGGSSS-SXXXXHHHHHHHHHHHHHHHHTTXH-HHHHHXEEEEXSXXXTTTHHHHHTSTTXXEEEESGGGGSHHHHHHHHHHHHHHHHX------- ->Q8ZJK9 -----------------------XXXXEEEEEXXS-----XXXHHHHHHHHHHHHHHHTT--XXSSEEEEEXXGGGHHHHHHHTTT--SSEEEEESXXXSXSSSSXTTXXXHHHHHHHTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHHTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHHHHXGGGGTTXEEEEXXGGGSSS-SXXXXHHHHHHHHHHHHHHHHTTXH-HHHHHXEEEEXSXXXTTTHHHHHTSTTXXEEEESGGGGSHHHHHHHHHHHHHHTTX------- ->A1RUV7 -----------------------XXSSEEEEEXTTXGGGSTHHHHHHHHHHHHHHHHH------TXEEEEEXXTTTHHHHHTTX-----SSXBEESXXSBSSXSSXTTXXBHHHHHHTTXXEEEESXTTSXXXHHHHHHHHHH----HHHTTXEEEEEESSHHHHHHHH--------------------TTXXSEEEEXXGGGTTS-SXXHHHHXHHHHHHHHHHHHHH------XTTSEEEEESSXXSHHHHHHHHHTTXSEEEEXHHHHTXSSHHHHHHHHHTHHHHTTSXX-- ->Q97VM8 -----------------------XXSSEEEEEXTTXTTSSHHHHHHHHHHHHHHHHHH------TXXEEEEEXGGGHHHHHHHX-----SSXEEESXXXXXXSSSXTTXXXHHHHHHTTXSEEEESXTTSXXXHHHHHHHHHH----HHHTTXEEEEEESSGGGHHHHH--------------------TTXXSEEEEXXGGGTTS-SXXHHHHXHHHHHHHHHHHTTS-------SSXEEEEXSSXXSHHHHHHHHHTTXSEEEESHHHHTXSSHHHHHHHHHHHHHHHHXX--- ->Q4JCD8 -----------------------XXSSEEEEEXXSXGGGSHHHHHHHHHHHHHHHHHT------TXXEEEEEXGGGHHHHHHHX-----XSEEEESXXXXSXSSSXTTXXXHHHHHHTTXXEEEESXTTSXXXHHHHHHHHHH----HHHTTXEEEEEESSGGGHHHHH--------------------TTXXSEEEEXXGGGTTS-SXXHHHHXHHHHHHHHHHHTTS-------SSXEEEEXSSXXSHHHHHHHHHTTXSEEEESHHHHTXSXHHHHHHHHHHHHHHHHHHHTX diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/merged_finalMSA_alignment.fasta b/toy_example/results/toy_example_2023_12_07_20_58_09/msas/merged_finalMSA_alignment.fasta deleted file mode 100644 index 2422a15..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/merged_finalMSA_alignment.fasta +++ /dev/null @@ -1,22 +0,0 @@ ->P72484 ----------------------MSRKPIIAGNWK-----MNKTAAEAREFIDAVKNNI-P--SNNLVDTVIGSPALFLEGMKKGVK--GTELQVAAQNCYWEDFGAFTGETSPAALAALGVDYVIIGHSERRDYFHETDQEINKKAHAIFKHKMTPILCCGESLETYEAGKTAEWIEGQITADLKGLSAEQVSSMVIAYEPIWAI-GTGKSADANIADDICGVVRATVEKLYGKEVAQAVRIQYGGSVKPENVAEYMAKENVDGALVGGASLQADSFLALLDF-VK------------ ->A5FRB6 -----------------------MRQIIIAGNWK-----MNTTLSEACTLVQSMKCEL-E--RIEGIEKIICPPFISLYPIKTMLE--NSSIKLGAQNLFYQEKGAYTGEISPLMLKEL-CQYVIIGHSERRAYFGETGQVVNQKIKAALQAGLLPIVCVGEKPEENENGQTRQVLETQLKEALDGLN--L-SCIIIAYEPIWAI-GTGKAATASEANSAIGYIRRVLGDTLGNAAAQTSPILYGGSVNEKNITEILSQTNIDGALVGGASLKAESFVSICRQAAVIQ-NKH------ ->A0QHY3 ----------------------MSRKPLIAGNWK-----MNLNHFEAIALVQKIAFAL-PDKYYDKVDVTVLPPFTDLRSVQTLVDGDKLRLSYGAQDLSQHDSGAYTGDISGAFLAKLGCTFVVVGHSERRTYHNEDDALVAAKAAAALKHELTPIICIGEHLEVREAGNHVIHCEEQLRGSLAGLSAEQIGKVVIAYEPVWAI-GTGRVASASDAQEVCAAIRKELASLASAQIADSVRVLYGGSVNAKNVGELIAQDDIDGGLVGGASLDGEQFATLAAIAAGGP-L-P------ ->P9WG42 ----------------------MSRKPLIAGNWK-----MNLNHYEAIALVQKIAFSL-PDKYYDRVDVAVIPPFTDLRSVQTLVDGDKLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAI-GTGRVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGGASLDGEHFATLAAIAAGGP-L-P------ ->Q3KM32 -MFTDKETHRKPFPTWAHLLHSEPSKQFVFGNWK-----MNKTLTEAQTFLKSFISSDIL--SNPQIITGIIPPFTLLSACQQAVS--DSPIFLGAQTTHEADSGAFTGEISAPMLKDIGVDFVLIGHSERRHIFHEQNPVLAEKAAAAIHSGMIPVLCIGETLEEQESGATQDILLNQLTIGLSKLPEQA--SFILAYEPVWAI-GTGKVAHPDLVQETHAFCRKTIASLFSKDIAERTPILYGGSVKADDARSLSLCPDVNGLLVGGASLSSENFLSIIQQVDIP----------- ->A0R756 -------------MPDARA-L-GAAQLWIGTSWK-----MNKGLAESRGYARELAEYV-AAKPPAGVQPFIIPSFTALTTVRDALGD-DSPVLLGVQNAHWEDHGAWTGEVSVAQAKDAGAQIVEIGHSERREHFGETVETTRLKVAAALHHGLVPLLCIGESAENKQAGESSRFILEQAAGALEGLTDEHLARVLIAYEPIWAIGENGRPATVEELRQPFDDLAREYG-----CR--TMGLLYGGSVNTDNAEDLLGIDHVTGLFIGRAAWQLPGYVRILEMAAAHPKAKA------ ->Q8Z2Y2 -----------------------MRHPLVMGNWK-----LNGSRHMVNELVANLRKEL-T--GVAGCDVAIAPPEMYIDLAKRAAA--GSHIMLGAQNVDLNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDTVLKTQGAAAFEGAVIAYEPVWAI-GTGKSATPAQAQAVHKFIRDHIAKA-DAKIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFAVIVKAAEAAK-Q-A------ ->Q8ZJK9 -----------------------MRHPLVMGNWK-----LNGSTHMVNELIAGLRKEL-S--TVDGCGVAIAPPAIYLNQAKHELA--GSRIALGAQNVDVNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHQESDELIAKKFGVLKEIGLIPVLCIGESEAENEAGQTEAVCAKQLDAVLNTLGVKAFEGAVIAYEPIWAI-GTGKSATPAQAQAVHKFIRDHIAKQ-DAAVAAQVIIQYGGSVNDKNAAELFTQPDIDGALVGGASLKADAFAVIVKAAAKAK-K-A------ ->A1RUV7 -----------------------MKFPILIINLKAYGEAAGKKALEIAKAAEKVAKEL-------GVNIAVAPNHLELALVAQSVE-----IPVYAQGADVETPGAYTAHIAVDNIKAVGASGLILNHSEAPLALNQLSKLAAR----AKSIGLDVVICAPDPVTS--------------------LAAAALGPHAVAVEPPELI-GTGKAVSKYKPETIIETVRLVTK------HFPNVVVITGAGIETGEDVEAALKLGTKGVLLASAAVKAKDHYQKIFELAKPL-TVAAEP--P ->Q97VM8 -----------------------MKPPIIIINFKAYENSFGDKAVNLGKKIEKISKEY-------SVEIILSTPATMIYRMSQEVD-----LPIYAEHVDPVPLGAFTGAILPEMVKDAGAKGTLINHSERRLRADEIDDVLKR----TKKLGLKSILCVDRYELV--------------------YPFSLLKPDAILIEPPELI-GTGVSVSKAKPEVITRAVDEIRK-------SEGIYLIAGAGITTGEDVYKALKLGAHGIGVASAVMKAKEPEKVVEDFITSA-LRAISS--- ->Q4JCD8 -----------------------MKPPVILINYKAYENSYGKKSIEITKKIEKVSKEY-------GTEIIVSVPATMIHRISEESE-----LTVFAQHVDSGEQGARTGAILPEMIKDAGARGSLLNHSERRIRLDEMAESLER----IRVLNLESVVCVDRYELV--------------------LPVALLRPNAVLIEPPELI-GTGIPVSKAKPEAITKAVEEIKK-------TKDVYLLAGAGITTGEDVFKAIELGADGIGAASAVMKAKEPEKVVEDFVKNA-IKAMEKRGE diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/squeezed_merged_finalMSA_alignment.fasta b/toy_example/results/toy_example_2023_12_07_20_58_09/msas/squeezed_merged_finalMSA_alignment.fasta deleted file mode 100644 index 7b88196..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/squeezed_merged_finalMSA_alignment.fasta +++ /dev/null @@ -1,22 +0,0 @@ ->P72484 ----------------------MSRKPIIAGNWKM-----NKTAAEAREFIDAVKNNIPS--NNLVDTVIGSPALFLEGMKKGVKG--TELQVAAQNCYWEDFGAFTGETSPAALAALGVDYVIIGHSERRDYFHETDQEINKKAHAIFKHKMTPILCCGESLETYEAGKTAEWIEGQITADLKGLSAEQVSSMVIAYEPIWAIGT-GKSADANIADDICGVVRATVEKLYGKEVAQAVRIQYGGSVKPENVAEYMAKENVDGALVGGASLQADSFLALLDFVK------------ ->A5FRB6 -----------------------MRQIIIAGNWKM-----NTTLSEACTLVQSMKCELER--IEGIEKIICPPFISLYPIKTMLEN--SSIKLGAQNLFYQEKGAYTGEISPLMLKEL-CQYVIIGHSERRAYFGETGQVVNQKIKAALQAGLLPIVCVGEKPEENENGQTRQVLETQ---LKEALDGLNLSCIIIAYEPIWAIGT-GKAATASEANSAIGYIRRVLGDTLGNAAAQTSPILYGGSVNEKNITEILSQTNIDGALVGGASLKAESFVSICRQAAVIQNKH------ ->A0QHY3 ----------------------MSRKPLIAGNWKM-----NLNHFEAIALVQKIAFALPDKYYDKVDVTVLPPFTDLRSVQTLVDGDKLRLSYGAQDLSQHDSGAYTGDISGAFLAKLGCTFVVVGHSERRTYHNEDDALVAAKAAAALKHELTPIICIGEHLEVREAGNHVIHCEEQLRGSLAGLSAEQIGKVVIAYEPVWAIGT-GRVASASDAQEVCAAIRKELASLASAQIADSVRVLYGGSVNAKNVGELIAQDDIDGGLVGGASLDGEQFATLAAIAAGGPLP------- ->P9WG42 ----------------------MSRKPLIAGNWKM-----NLNHYEAIALVQKIAFSLPDKYYDRVDVAVIPPFTDLRSVQTLVDGDKLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIGT-GRVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGGASLDGEHFATLAAIAAGGPLP------- ->Q3KM32 -MFTDKETHRKPFPTWAHLLHSEPSKQFVFGNWKM-----NKTLTEAQTFLKSFISSDILS-NPQIITGIIPPFTLLSACQQAVSD--SPIFLGAQTTHEADSGAFTGEISAPMLKDIGVDFVLIGHSERRHIFHEQNPVLAEKAAAAIHSGMIPVLCIGETLEEQESGATQDILLNQ--LTIGLSKLPEQASFILAYEPVWAIGT-GKVAHPDLVQETHAFCRKTIASLFSKDIAERTPILYGGSVKADDARSLSLCPDVNGLLVGGASLSSENFLSIIQQVDIP---------- ->A0R756 ---------------MPDARALGAAQLWIGTSWKM-----NKGLAESRGYARELAEYVAAKPPAGVQPFIIPSFTALTTVRDALGD-DSPVLLGVQNAHWEDHGAWTGEVSVAQAKDAGAQIVEIGHSERREHFGETVETTRLKVAAALHHGLVPLLCIGESAENKQAGESSRFILEQAAGALEGLTDEHLARVLIAYEPIWAIGENGRPATVEELRQPFDDLAREYGC-------RTMGLLYGGSVNTDNAEDLLGIDHVTGLFIGRAAWQLPGYVRILEMAAAHPKAKA----- ->Q8Z2Y2 -----------------------MRHPLVMGNWKL-----NGSRHMVNELVANLRKELTG--VAGCDVAIAPPEMYIDLAKRAAAG--SHIMLGAQNVDLNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDTVLKTQGAAAFEGAVIAYEPVWAIGT-GKSATPAQAQAVHKFIRDHIAKADA-KIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFAVIVKAAEAAKQA------- ->Q8ZJK9 -----------------------MRHPLVMGNWKL-----NGSTHMVNELIAGLRKELST--VDGCGVAIAPPAIYLNQAKHELAG--SRIALGAQNVDVNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHQESDELIAKKFGVLKEIGLIPVLCIGESEAENEAGQTEAVCAKQLDAVLNTLGVKAFEGAVIAYEPIWAIGT-GKSATPAQAQAVHKFIRDHIAKQDA-AVAAQVIIQYGGSVNDKNAAELFTQPDIDGALVGGASLKADAFAVIVKAAAKAKKA------- ->A1RUV7 -----------------------MKFPILIINLKAYGEAAGKKALEIAKAAEKVAKEL------GVNIAVAPNHLELALVAQSV-----EIPVYAQGADVETPGAYTAHIAVDNIKAVGASGLILNHSEAPLALNQLSKLAAR----AKSIGLDVVICAPDPVTSLAAA--------------------ALGPHAVAVEPPELIGT-GKAVSKYKPETIIETVRLVTKH------FPNVVVITGAGIETGEDVEAALKLGTKGVLLASAAVKAKDHYQKIFELAKPLTVAAEPP-- ->Q97VM8 -----------------------MKPPIIIINFKAYENSFGDKAVNLGKKIEKISKEY------SVEIILSTPATMIYRMSQEV-----DLPIYAEHVDPVPLGAFTGAILPEMVKDAGAKGTLINHSERRLRADEIDDVLKR----TKKLGLKSILCVDRYELVYPFS--------------------LLKPDAILIEPPELIGT-GVSVSKAKPEVITRAVDEIRKS-------EGIYLIAGAGITTGEDVYKALKLGAHGIGVASAVMKAKEPEKVVEDFITSALRAISS--- ->Q4JCD8 -----------------------MKPPVILINYKAYENSYGKKSIEITKKIEKVSKEY------GTEIIVSVPATMIHRISEES-----ELTVFAQHVDSGEQGARTGAILPEMIKDAGARGSLLNHSERRIRLDEMAESLER----IRVLNLESVVCVDRYELVLPVA--------------------LLRPNAVLIEPPELIGT-GIPVSKAKPEAITKAVEEIKKT-------KDVYLLAGAGITTGEDVFKAIELGADGIGAASAVMKAKEPEKVVEDFVKNAIKAMEKRGE diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/t-coffee/aligned_Subset0.aln b/toy_example/results/toy_example_2023_12_07_20_58_09/msas/t-coffee/aligned_Subset0.aln deleted file mode 100644 index e3c8cd9..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/t-coffee/aligned_Subset0.aln +++ /dev/null @@ -1,64 +0,0 @@ -CLUSTAL FORMAT for T-COFFEE Version_13.45.61.3c310a9 [http://www.tcoffee.org] [MODE: 3dcoffee ], CPU=0.00 sec, SCORE=98, Nseq=8, Len=286 - -P72484 ---------------------MSRKPIIAGNWKMNKTAAEAREFIDAVKN -A5FRB6 ----------------------MRQIIIAGNWKMNTTLSEACTLVQSMKC -A0QHY3 ---------------------MSRKPLIAGNWKMNLNHFEAIALVQKIAF -P9WG42 ---------------------MSRKPLIAGNWKMNLNHYEAIALVQKIAF -Q3KM32 MFTDKETHRKPFPTWAHLLHSEPSKQFVFGNWKMNKTLTEAQTFLKSFIS -A0R756 ------------MPDARA-L-GAAQLWIGTSWKMNKGLAESRGYARELAE -Q8Z2Y2 ----------------------MRHPLVMGNWKLNGSRHMVNELVANLRK -Q8ZJK9 ----------------------MRHPLVMGNWKLNGSTHMVNELIAGLRK - : : .**:* . - -P72484 NI-P--SNNLVDTVIGSPALFLEGMKKGVK--GTELQVAAQNCYWEDFGA -A5FRB6 EL-E--RIEGIEKIICPPFISLYPIKTMLE--NSSIKLGAQNLFYQEKGA -A0QHY3 AL-PDKYYDKVDVTVLPPFTDLRSVQTLVDGDKLRLSYGAQDLSQHDSGA -P9WG42 SL-PDKYYDRVDVAVIPPFTDLRSVQTLVDGDKLRLTYGAQDLSPHDSGA -Q3KM32 SDIL--SNPQIITGIIPPFTLLSACQQAVS--DSPIFLGAQTTHEADSGA -A0R756 YV-AAKPPAGVQPFIIPSFTALTTVRDALGD-DSPVLLGVQNAHWEDHGA -Q8Z2Y2 EL-T--GVAGCDVAIAPPEMYIDLAKRAAA--GSHIMLGAQNVDLNLSGA -Q8ZJK9 EL-S--TVDGCGVAIAPPAIYLNQAKHELA--GSRIALGAQNVDVNLSGA - : .. : : : ..* ** - -P72484 FTGETSPAALAALGVDYVIIGHSERRDYFHETDQEINKKAHAIFKHKMTP -A5FRB6 YTGEISPLMLKEL-CQYVIIGHSERRAYFGETGQVVNQKIKAALQAGLLP -A0QHY3 YTGDISGAFLAKLGCTFVVVGHSERRTYHNEDDALVAAKAAAALKHELTP -P9WG42 YTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATALKHGLTP -Q3KM32 FTGEISAPMLKDIGVDFVLIGHSERRHIFHEQNPVLAEKAAAAIHSGMIP -A0R756 WTGEVSVAQAKDAGAQIVEIGHSERREHFGETVETTRLKVAAALHHGLVP -Q8Z2Y2 FTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTP -Q8ZJK9 FTGETSAEMLKDIGAQYIIIGHSERRTYHQESDELIAKKFGVLKEIGLIP - :**: * : :****** . * * . . : * - -P72484 ILCCGESLETYEAGKTAEWIEGQITADLKGLSAEQVSSMVIAYEPIWAI- -A5FRB6 IVCVGEKPEENENGQTRQVLETQLKEALDGLN--L-SCIIIAYEPIWAI- -A0QHY3 IICIGEHLEVREAGNHVIHCEEQLRGSLAGLSAEQIGKVVIAYEPVWAI- -P9WG42 IVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAI- -Q3KM32 VLCIGETLEEQESGATQDILLNQLTIGLSKLPEQA--SFILAYEPVWAI- -A0R756 LLCIGESAENKQAGESSRFILEQAAGALEGLTDEHLARVLIAYEPIWAIG -Q8Z2Y2 VLCIGETEAENEAGKTEEVCARQIDTVLKTQGAAAFEGAVIAYEPVWAI- -Q8ZJK9 VLCIGESEAENEAGQTEAVCAKQLDAVLNTLGVKAFEGAVIAYEPIWAI- - ::* ** : * * * ::****:*** - -P72484 GTGKSADANIADDICGVVRATVEKLYGKEVAQAVRIQYGGSVKPENVAEY -A5FRB6 GTGKAATASEANSAIGYIRRVLGDTLGNAAAQTSPILYGGSVNEKNITEI -A0QHY3 GTGRVASASDAQEVCAAIRKELASLASAQIADSVRVLYGGSVNAKNVGEL -P9WG42 GTGRVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDI -Q3KM32 GTGKVAHPDLVQETHAFCRKTIASLFSKDIAERTPILYGGSVKADDARSL -A0R756 ENGRPATVEELRQPFDDLAREYG-----CR--TMGLLYGGSVNTDNAEDL -Q8Z2Y2 GTGKSATPAQAQAVHKFIRDHIAKA-DAKIAEQVIIQYGGSVNASNAAEL -Q8ZJK9 GTGKSATPAQAQAVHKFIRDHIAKQ-DAAVAAQVIIQYGGSVNDKNAAEL - .*: * : *****: .: . - -P72484 MAKENVDGALVGGASLQADSFLALLDF-VK------ -A5FRB6 LSQTNIDGALVGGASLKAESFVSICRQAAVIQ-NKH -A0QHY3 IAQDDIDGGLVGGASLDGEQFATLAAIAAGGP-L-P -P9WG42 VAQDDVDGGLVGGASLDGEHFATLAAIAAGGP-L-P -Q3KM32 SLCPDVNGLLVGGASLSSENFLSIIQQVDIP----- -A0R756 LGIDHVTGLFIGRAAWQLPGYVRILEMAAAHPKAKA -Q8Z2Y2 FAQPDIDGALVGGASLKADAFAVIVKAAEAAK-Q-A -Q8ZJK9 FTQPDIDGALVGGASLKADAFAVIVKAAAKAK-K-A - .: * ::* *: . : : - - - diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/t-coffee/aligned_Subset1.aln b/toy_example/results/toy_example_2023_12_07_20_58_09/msas/t-coffee/aligned_Subset1.aln deleted file mode 100644 index 1997025..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/t-coffee/aligned_Subset1.aln +++ /dev/null @@ -1,29 +0,0 @@ -CLUSTAL FORMAT for T-COFFEE Version_13.45.61.3c310a9 [http://www.tcoffee.org] [MODE: 3dcoffee ], CPU=0.00 sec, SCORE=99, Nseq=3, Len=231 - -A1RUV7 MKFPILIINLKAYGEAAGKKALEIAKAAEKVAKELGVNIAVAPNHLELAL -Q97VM8 MKPPIIIINFKAYENSFGDKAVNLGKKIEKISKEYSVEIILSTPATMIYR -Q4JCD8 MKPPVILINYKAYENSYGKKSIEITKKIEKVSKEYGTEIIVSVPATMIHR - ** *:::** *** :: *.*:::: * **::** ..:* :: : - -A1RUV7 VAQSVEIPVYAQGADVETPGAYTAHIAVDNIKAVGASGLILNHSEAPLAL -Q97VM8 MSQEVDLPIYAEHVDPVPLGAFTGAILPEMVKDAGAKGTLINHSERRLRA -Q4JCD8 ISEESELTVFAQHVDSGEQGARTGAILPEMIKDAGARGSLLNHSERRIRL - :::. ::.::*: .* ** *. * : :* .** * ::**** : - -A1RUV7 NQLSKLAARAKSIGLDVVICAPDPVTSLAAAALGPHAVAVEPPELIGTGK -Q97VM8 DEIDDVLKRTKKLGLKSILCVDRYELVYPFSLLKPDAILIEPPELIGTGV -Q4JCD8 DEMAESLERIRVLNLESVVCVDRYELVLPVALLRPNAVLIEPPELIGTGI - ::: . * : :.*. ::*. . : * *.*: :********* - -A1RUV7 AVSKYKPETIIETVRLVTKHFPNVVVITGAGIETGEDVEAALKLGTKGVL -Q97VM8 SVSKAKPEVITRAVDEIRK-SEGIYLIAGAGITTGEDVYKALKLGAHGIG -Q4JCD8 PVSKAKPEAITKAVEEIKK-TKDVYLLAGAGITTGEDVFKAIELGADGIG - .*** ***.* .:* : * .: :::**** ***** *::**:.*: - -A1RUV7 LASAAVKAKDHYQKIFELAKPLTVAAEP--P -Q97VM8 VASAVMKAKEPEKVVEDFITSALRAISS--- -Q4JCD8 AASAVMKAKEPEKVVEDFVKNAIKAMEKRGE - ***.:***: : : :: . * . - - - diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/unmappable_dssp.fasta b/toy_example/results/toy_example_2023_12_07_20_58_09/msas/unmappable_dssp.fasta deleted file mode 100644 index 1070185..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/msas/unmappable_dssp.fasta +++ /dev/null @@ -1,4 +0,0 @@ ->Q3ZXC5 -XXXXEEEEEXXSXXXHHHHHHHHHHHHHHHHTXXSSEEEEEXXHHHHHHHHHHTTTXSXEEEESXXXSSSSSSXTTXXXHHHHTTTXSEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHTTXXXSXXEEEEXXGGGSSSSXXXXHHHHHHHHHHHHHHHHHHHXHHHHHHXXEEEXSSXXTTTHHHHHTSTTXXEEEESGGGGSHHHHHHHHHHHHHHHTTX ->O84332 -XXXXXXXXXXXXXXHHHHHHSXTTXEEEEEEXXSXXXHHHHHHHHHHHTTXGGGGXTTEEEEEEXXGGGHHHHHHHHTTSSXEEEESXXBSSSSSSXTTXXBHHHHHHHTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHTTSXTTXXXEEEEXXGGGTTTXXXXXHHHHHHHHHHHHHHHHHHSXHHHHHHSXEEEXSSXXHHHHHHHHTSTTXXEEEEXGGGGSHHHHHHHHHHXXXX diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/reordered_squeezed_merged_finalMSA_alignment.fasta b/toy_example/results/toy_example_2023_12_07_20_58_09/reordered_squeezed_merged_finalMSA_alignment.fasta deleted file mode 100644 index 3447756..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/reordered_squeezed_merged_finalMSA_alignment.fasta +++ /dev/null @@ -1,22 +0,0 @@ ->A1RUV7 -----------------------MKFPILIINLKAYGEAAGKKALEIAKAAEKVAKEL------GVNIAVAPNHLELALVAQSV-----EIPVYAQGADVETPGAYTAHIAVDNIKAVGASGLILNHSEAPLALNQLSKLAAR----AKSIGLDVVICAPDPVTSLAAA--------------------ALGPHAVAVEPPELIGT-GKAVSKYKPETIIETVRLVTKH------FPNVVVITGAGIETGEDVEAALKLGTKGVLLASAAVKAKDHYQKIFELAKPLTVAAEPP-- ->P72484 ----------------------MSRKPIIAGNWKM-----NKTAAEAREFIDAVKNNIPS--NNLVDTVIGSPALFLEGMKKGVKG--TELQVAAQNCYWEDFGAFTGETSPAALAALGVDYVIIGHSERRDYFHETDQEINKKAHAIFKHKMTPILCCGESLETYEAGKTAEWIEGQITADLKGLSAEQVSSMVIAYEPIWAIGT-GKSADANIADDICGVVRATVEKLYGKEVAQAVRIQYGGSVKPENVAEYMAKENVDGALVGGASLQADSFLALLDFVK------------ ->A5FRB6 -----------------------MRQIIIAGNWKM-----NTTLSEACTLVQSMKCELER--IEGIEKIICPPFISLYPIKTMLEN--SSIKLGAQNLFYQEKGAYTGEISPLMLKEL-CQYVIIGHSERRAYFGETGQVVNQKIKAALQAGLLPIVCVGEKPEENENGQTRQVLETQ---LKEALDGLNLSCIIIAYEPIWAIGT-GKAATASEANSAIGYIRRVLGDTLGNAAAQTSPILYGGSVNEKNITEILSQTNIDGALVGGASLKAESFVSICRQAAVIQNKH------ ->A0QHY3 ----------------------MSRKPLIAGNWKM-----NLNHFEAIALVQKIAFALPDKYYDKVDVTVLPPFTDLRSVQTLVDGDKLRLSYGAQDLSQHDSGAYTGDISGAFLAKLGCTFVVVGHSERRTYHNEDDALVAAKAAAALKHELTPIICIGEHLEVREAGNHVIHCEEQLRGSLAGLSAEQIGKVVIAYEPVWAIGT-GRVASASDAQEVCAAIRKELASLASAQIADSVRVLYGGSVNAKNVGELIAQDDIDGGLVGGASLDGEQFATLAAIAAGGPLP------- ->P9WG42 ----------------------MSRKPLIAGNWKM-----NLNHYEAIALVQKIAFSLPDKYYDRVDVAVIPPFTDLRSVQTLVDGDKLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIGT-GRVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGGASLDGEHFATLAAIAAGGPLP------- ->Q3KM32 -MFTDKETHRKPFPTWAHLLHSEPSKQFVFGNWKM-----NKTLTEAQTFLKSFISSDILS-NPQIITGIIPPFTLLSACQQAVSD--SPIFLGAQTTHEADSGAFTGEISAPMLKDIGVDFVLIGHSERRHIFHEQNPVLAEKAAAAIHSGMIPVLCIGETLEEQESGATQDILLNQ--LTIGLSKLPEQASFILAYEPVWAIGT-GKVAHPDLVQETHAFCRKTIASLFSKDIAERTPILYGGSVKADDARSLSLCPDVNGLLVGGASLSSENFLSIIQQVDIP---------- ->A0R756 ---------------MPDARALGAAQLWIGTSWKM-----NKGLAESRGYARELAEYVAAKPPAGVQPFIIPSFTALTTVRDALGD-DSPVLLGVQNAHWEDHGAWTGEVSVAQAKDAGAQIVEIGHSERREHFGETVETTRLKVAAALHHGLVPLLCIGESAENKQAGESSRFILEQAAGALEGLTDEHLARVLIAYEPIWAIGENGRPATVEELRQPFDDLAREYGC-------RTMGLLYGGSVNTDNAEDLLGIDHVTGLFIGRAAWQLPGYVRILEMAAAHPKAKA----- ->Q8Z2Y2 -----------------------MRHPLVMGNWKL-----NGSRHMVNELVANLRKELTG--VAGCDVAIAPPEMYIDLAKRAAAG--SHIMLGAQNVDLNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDTVLKTQGAAAFEGAVIAYEPVWAIGT-GKSATPAQAQAVHKFIRDHIAKADA-KIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFAVIVKAAEAAKQA------- ->Q8ZJK9 -----------------------MRHPLVMGNWKL-----NGSTHMVNELIAGLRKELST--VDGCGVAIAPPAIYLNQAKHELAG--SRIALGAQNVDVNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHQESDELIAKKFGVLKEIGLIPVLCIGESEAENEAGQTEAVCAKQLDAVLNTLGVKAFEGAVIAYEPIWAIGT-GKSATPAQAQAVHKFIRDHIAKQDA-AVAAQVIIQYGGSVNDKNAAELFTQPDIDGALVGGASLKADAFAVIVKAAAKAKKA------- ->Q97VM8 -----------------------MKPPIIIINFKAYENSFGDKAVNLGKKIEKISKEY------SVEIILSTPATMIYRMSQEV-----DLPIYAEHVDPVPLGAFTGAILPEMVKDAGAKGTLINHSERRLRADEIDDVLKR----TKKLGLKSILCVDRYELVYPFS--------------------LLKPDAILIEPPELIGT-GVSVSKAKPEVITRAVDEIRKS-------EGIYLIAGAGITTGEDVYKALKLGAHGIGVASAVMKAKEPEKVVEDFITSALRAISS--- ->Q4JCD8 -----------------------MKPPVILINYKAYENSYGKKSIEITKKIEKVSKEY------GTEIIVSVPATMIHRISEES-----ELTVFAQHVDSGEQGARTGAILPEMIKDAGARGSLLNHSERRIRLDEMAESLER----IRVLNLESVVCVDRYELVLPVA--------------------LLRPNAVLIEPPELIGT-GIPVSKAKPEAITKAVEEIKKT-------KDVYLLAGAGITTGEDVFKAIELGADGIGAASAVMKAKEPEKVVEDFVKNAIKAMEKRGE diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/run_report_toy_example_2023_12_07_20_58_09_test.nflog b/toy_example/results/toy_example_2023_12_07_20_58_09/run_report_toy_example_2023_12_07_20_58_09_test.nflog deleted file mode 100644 index 15329ff..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/run_report_toy_example_2023_12_07_20_58_09_test.nflog +++ /dev/null @@ -1,1232 +0,0 @@ -N E X T F L O W ~ version 23.04.2 -Launching `simsapiper.nf` [romantic_carlsson] DSL2 - revision: a5a791e441 - -Usage: - -$ nextflow run simsapiper.nf -profile server,withsingularity --magic - -================================================================================ - LIST OF PARAMETERS -================================================================================ - GENERAL - -Launch dir : /rhea/scratch/brussel/106/vsc10611/simsapiper -Project dir : /rhea/scratch/brussel/106/vsc10611/simsapiper -Execution time : 2023_12_07_20_58_12 -================================================================================ - INPUT FILES - -Input file folder (--data): /scratch/brussel/106/vsc10611/simsapiper/toy_example/data -Input sequence format (--seqFormat fasta): fasta - !Find all possible formats at https://biopython.org/wiki/SeqIO -Ignore sequences with % unknown characters (--seqQC 5): 5 -Collapse sequences with % sequence identity (--dropSimilar 90): 90 -================================================================================ - OUTPUT FILES - -Output folder: /scratch/brussel/106/vsc10611/simsapiper/results/toy_example_2023_12_07_20_58_09_test -Final MSA file name (--outName mymsa): finalMSA -================================================================================ - SUBSETTING - -Creates subsets of % sequence identity (--createSubsets 30): 30 -Set minimal % sequence identity in subsets (--minSubsetID 20): 20 - !Reduce the number of subsets by collating with --minSubsetID "min" -Set maximal size of subset(--maxSubsetSize 100): true - -User provides fasta files with subsets (--useSubsets): false - !Provide sequences not fitting any subset in a file containing 'orphan' in filename -================================================================================ - ADD STRUCTURAL INFORMATION - -Retrieve protein structure models from AFDB (--retrieve): true -Predict protein structure models with ESM Atlas (--model): true -Maximal % of sequences not matched to a model (--strucQC 5): 5 -================================================================================ - ALINGMENT PARAMETERS - -Additional parameters for Tcoffee (--tcoffeeParams): false -Additional parameters for MAFFT (--mafftParams "--localpair --maxiterate 1000"): false -Map DSSP to alignment (--dssp): true -Squeeze alignment towards anchors (--squeeze "H,E"): H,G,E - !Select secondary structure elements for anchor points according to DSSP annotation -Set minimal occurence % of anchor element in MSA: (--squeezePerc 80): 80 -Order MSA by input files (--reorder "cluster3.fasta,cluster4.fasta"): true -Convert final MSA output from fasta (--convertMSA clustal): false -================================================================================ - -[- ] process > convertSeqs - -[- ] process > cdHitCollapse - -[- ] process > writeFastaFromSeqsInvalid - - -[- ] process > convertSeqs - -[- ] process > cdHitCollapse - -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[- ] process > missingQC - -[- ] process > writeFastaFromFound - -[- ] process > cdHitSubsetting - -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[- ] process > runDssp - -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta - -[- ] process > convertSeqs [ 0%] 0 of 1 -[- ] process > cdHitCollapse - -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[- ] process > missingQC - -[- ] process > writeFastaFromFound - -[- ] process > cdHitSubsetting - -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[- ] process > runDssp - -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta - -executor > slurm (1) -[54/ab579f] process > convertSeqs (1) [ 0%] 0 of 1 -[- ] process > cdHitCollapse - -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[- ] process > missingQC - -[- ] process > writeFastaFromFound - -[- ] process > cdHitSubsetting - -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[- ] process > runDssp - -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta - -executor > slurm (1) -[54/ab579f] process > convertSeqs (1) [ 0%] 0 of 1 -[- ] process > cdHitCollapse - -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[- ] process > missingQC - -[- ] process > writeFastaFromFound - -[- ] process > cdHitSubsetting - -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[- ] process > runDssp - -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta - -executor > slurm (1) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[- ] process > cdHitCollapse - -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[- ] process > missingQC - -[- ] process > writeFastaFromFound - -[- ] process > cdHitSubsetting - -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[- ] process > runDssp - -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta - -executor > slurm (2) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [ 0%] 0 of 1 -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[- ] process > missingQC - -[- ] process > writeFastaFromFound - -[- ] process > cdHitSubsetting - -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[- ] process > runDssp - -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta - -executor > slurm (2) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[- ] process > missingQC [ 0%] 0 of 1 -[- ] process > writeFastaFromFound [ 0%] 0 of 1 -[- ] process > cdHitSubsetting - -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[- ] process > runDssp - -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (3) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [ 0%] 0 of 1 -[- ] process > writeFastaFromFound [ 0%] 0 of 1 -[- ] process > cdHitSubsetting - -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[- ] process > runDssp - -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (4) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [ 0%] 0 of 1 -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [ 0%] 0 of 1 -[- ] process > cdHitSubsetting - -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[- ] process > runDssp - -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (4) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[- ] process > runDssp [ 0%] 0 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (6) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[f6/5bedac] process > runDssp (9) [ 0%] 0 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (7) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[1a/9c4d1a] process > runDssp (1) [ 0%] 0 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (8) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[83/5947b0] process > runDssp (6) [ 0%] 0 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (9) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[ae/2dd3d6] process > runDssp (2) [ 0%] 0 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (10) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[21/90800d] process > runDssp (4) [ 0%] 0 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (11) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[be/971f0e] process > runDssp (3) [ 0%] 0 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (11) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[f6/5bedac] process > runDssp (9) [ 15%] 2 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (12) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[e2/26feb0] process > runDssp (7) [ 15%] 2 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (13) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[69/508a5f] process > runDssp (5) [ 15%] 2 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (14) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[d0/20ce94] process > runDssp (8) [ 15%] 2 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (15) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[e9/430a1a] process > runDssp (11) [ 15%] 2 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (15) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[21/90800d] process > runDssp (4) [ 46%] 6 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (15) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[e2/26feb0] process > runDssp (7) [ 61%] 8 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (17) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > cdHitSubsetting [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [ 61%] 8 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (18) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [ 61%] 8 of 13 -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (18) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [ 0%] 0 of 1 -[- ] process > runTcoffee - -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - -Sequence file found:/scratch/brussel/106/vsc10611/simsapiper/toy_example/data/seqs/toy_example_seqs.fasta -Number of sequences before collapsing:13 -Model without matching sequence:O84332 -Sequences to be aligned:11 -Model without matching sequence:Q3ZXC5 -Provided model matched:11 -Missing models: 0 - -executor > slurm (18) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[- ] process > runTcoffee [ 0%] 0 of 2 -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - - - - - - - - -executor > slurm (19) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [ 0%] 0 of 2 -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - - - - - - - - -executor > slurm (20) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[cd/4bf283] process > runTcoffee (Subset1.fasta) [ 0%] 0 of 2 -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (20) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[cd/4bf283] process > runTcoffee (Subset1.fasta) [ 0%] 0 of 2 -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (20) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[cd/4bf283] process > runTcoffee (Subset1.fasta) [ 50%] 1 of 2 -[- ] process > convertTCMsa - -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (20) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[- ] process > convertTCMsa [ 0%] 0 of 2 -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (21) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[1d/686267] process > convertTCMsa (2) [ 0%] 0 of 2 -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (22) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [ 0%] 0 of 2 -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (22) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[1d/686267] process > convertTCMsa (2) [ 50%] 1 of 2 -[- ] process > mergeMafft - -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (22) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[- ] process > mergeMafft [ 0%] 0 of 1 -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (23) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [ 0%] 0 of 1 -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (23) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [ 0%] 0 of 1 -[- ] process > attendance - -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough - -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (23) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[- ] process > attendance [ 0%] 0 of 1 -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[- ] process > mapDsspRough [ 0%] 0 of 1 -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (24) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[- ] process > attendance [ 0%] 0 of 1 -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[31/92f2ae] process > mapDsspRough [ 0%] 0 of 1 -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (25) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[b0/c7ac1f] process > attendance [ 0%] 0 of 1 -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[31/92f2ae] process > mapDsspRough [ 0%] 0 of 1 -[- ] process > squeeze - -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (25) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[b0/c7ac1f] process > attendance [100%] 1 of 1 ✔ -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[31/92f2ae] process > mapDsspRough [100%] 1 of 1 ✔ -[- ] process > squeeze [ 0%] 0 of 1 -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (26) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[b0/c7ac1f] process > attendance [100%] 1 of 1 ✔ -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[31/92f2ae] process > mapDsspRough [100%] 1 of 1 ✔ -[eb/a93340] process > squeeze [ 0%] 0 of 1 -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (26) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[b0/c7ac1f] process > attendance [100%] 1 of 1 ✔ -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[31/92f2ae] process > mapDsspRough [100%] 1 of 1 ✔ -[eb/a93340] process > squeeze [ 0%] 0 of 1 -[- ] process > mapDsspSqueeze - -[- ] process > reorder - - -executor > slurm (26) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[b0/c7ac1f] process > attendance [100%] 1 of 1 ✔ -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[31/92f2ae] process > mapDsspRough [100%] 1 of 1 ✔ -[eb/a93340] process > squeeze [100%] 1 of 1 ✔ -[- ] process > mapDsspSqueeze [ 0%] 0 of 1 -[- ] process > reorder [ 0%] 0 of 1 - -executor > slurm (27) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[b0/c7ac1f] process > attendance [100%] 1 of 1 ✔ -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[31/92f2ae] process > mapDsspRough [100%] 1 of 1 ✔ -[eb/a93340] process > squeeze [100%] 1 of 1 ✔ -[9d/8dac47] process > mapDsspSqueeze [ 0%] 0 of 1 -[- ] process > reorder [ 0%] 0 of 1 - -executor > slurm (28) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[b0/c7ac1f] process > attendance [100%] 1 of 1 ✔ -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[31/92f2ae] process > mapDsspRough [100%] 1 of 1 ✔ -[eb/a93340] process > squeeze [100%] 1 of 1 ✔ -[9d/8dac47] process > mapDsspSqueeze [ 0%] 0 of 1 -[d6/53981b] process > reorder [ 0%] 0 of 1 - -executor > slurm (28) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[b0/c7ac1f] process > attendance [100%] 1 of 1 ✔ -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[31/92f2ae] process > mapDsspRough [100%] 1 of 1 ✔ -[eb/a93340] process > squeeze [100%] 1 of 1 ✔ -[9d/8dac47] process > mapDsspSqueeze [ 0%] 0 of 1 -[d6/53981b] process > reorder [ 0%] 0 of 1 - -executor > slurm (28) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[b0/c7ac1f] process > attendance [100%] 1 of 1 ✔ -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[31/92f2ae] process > mapDsspRough [100%] 1 of 1 ✔ -[eb/a93340] process > squeeze [100%] 1 of 1 ✔ -[9d/8dac47] process > mapDsspSqueeze [100%] 1 of 1 ✔ -[d6/53981b] process > reorder [100%] 1 of 1 ✔ -Pipeline completed at : 2023-12-07T21:00:19.334137+01:00 -Time to complete workflow execution : 2m 7s -Execution status : Success -Output folder : /scratch/brussel/106/vsc10611/simsapiper/results/toy_example_2023_12_07_20_58_09_test - -executor > slurm (28) -[54/ab579f] process > convertSeqs (1) [100%] 1 of 1 ✔ -[ba/aa81b2] process > cdHitCollapse (converted_toy_example_seqs.fasta) [100%] 1 of 1 ✔ -[- ] process > writeFastaFromSeqsInvalid - -[- ] process > getAFmodels - -[- ] process > fetchEsmAtlasStructure - -[- ] process > writeFastaFromMissing - -[29/5d578e] process > missingQC [100%] 1 of 1 ✔ -[40/88c1bb] process > writeFastaFromFound (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[9d/89f9a7] process > cdHitSubsetting (seqs_to_align.fasta) [100%] 1 of 1 ✔ -[d5/9d880d] process > runTcoffee (Subset0.fasta) [100%] 2 of 2 ✔ -[d6/811910] process > convertTCMsa (1) [100%] 2 of 2 ✔ -[bd/5951a4] process > mergeMafft [100%] 1 of 1 ✔ -[b0/c7ac1f] process > attendance [100%] 1 of 1 ✔ -[79/d178d7] process > runDssp (13) [100%] 13 of 13 ✔ -[31/92f2ae] process > mapDsspRough [100%] 1 of 1 ✔ -[eb/a93340] process > squeeze [100%] 1 of 1 ✔ -[9d/8dac47] process > mapDsspSqueeze [100%] 1 of 1 ✔ -[d6/53981b] process > reorder [100%] 1 of 1 ✔ -Pipeline completed at : 2023-12-07T21:00:19.334137+01:00 -Time to complete workflow execution : 2m 7s -Execution status : Success -Output folder : /scratch/brussel/106/vsc10611/simsapiper/results/toy_example_2023_12_07_20_58_09_test -Completed at: 07-Dec-2023 21:00:20 -Duration : 2m 7s -CPU hours : 0.1 -Succeeded : 28 - - diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/seqs/CD-HIT_for_t-coffee/Subset1.fasta b/toy_example/results/toy_example_2023_12_07_20_58_09/seqs/CD-HIT_for_t-coffee/Subset1.fasta deleted file mode 100644 index b4c092d..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/seqs/CD-HIT_for_t-coffee/Subset1.fasta +++ /dev/null @@ -1,6 +0,0 @@ ->A1RUV7 -MKFPILIINLKAYGEAAGKKALEIAKAAEKVAKELGVNIAVAPNHLELALVAQSVEIPVYAQGADVETPGAYTAHIAVDNIKAVGASGLILNHSEAPLALNQLSKLAARAKSIGLDVVICAPDPVTSLAAAALGPHAVAVEPPELIGTGKAVSKYKPETIIETVRLVTKHFPNVVVITGAGIETGEDVEAALKLGTKGVLLASAAVKAKDHYQKIFELAKPLTVAAEPP ->Q97VM8 -MKPPIIIINFKAYENSFGDKAVNLGKKIEKISKEYSVEIILSTPATMIYRMSQEVDLPIYAEHVDPVPLGAFTGAILPEMVKDAGAKGTLINHSERRLRADEIDDVLKRTKKLGLKSILCVDRYELVYPFSLLKPDAILIEPPELIGTGVSVSKAKPEVITRAVDEIRKSEGIYLIAGAGITTGEDVYKALKLGAHGIGVASAVMKAKEPEKVVEDFITSALRAISS ->Q4JCD8 -MKPPVILINYKAYENSYGKKSIEITKKIEKVSKEYGTEIIVSVPATMIHRISEESELTVFAQHVDSGEQGARTGAILPEMIKDAGARGSLLNHSERRIRLDEMAESLERIRVLNLESVVCVDRYELVLPVALLRPNAVLIEPPELIGTGIPVSKAKPEAITKAVEEIKKTKDVYLLAGAGITTGEDVFKAIELGADGIGAASAVMKAKEPEKVVEDFVKNAIKAMEKRGE diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/seqs/converted_aligned_Subset0.fasta b/toy_example/results/toy_example_2023_12_07_20_58_09/seqs/converted_aligned_Subset0.fasta deleted file mode 100644 index de87f21..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/seqs/converted_aligned_Subset0.fasta +++ /dev/null @@ -1,16 +0,0 @@ ->P72484 ----------------------MSRKPIIAGNWKMNKTAAEAREFIDAVKNNI-P--SNNLVDTVIGSPALFLEGMKKGVK--GTELQVAAQNCYWEDFGAFTGETSPAALAALGVDYVIIGHSERRDYFHETDQEINKKAHAIFKHKMTPILCCGESLETYEAGKTAEWIEGQITADLKGLSAEQVSSMVIAYEPIWAI-GTGKSADANIADDICGVVRATVEKLYGKEVAQAVRIQYGGSVKPENVAEYMAKENVDGALVGGASLQADSFLALLDF-VK------ ->A5FRB6 -----------------------MRQIIIAGNWKMNTTLSEACTLVQSMKCEL-E--RIEGIEKIICPPFISLYPIKTMLE--NSSIKLGAQNLFYQEKGAYTGEISPLMLKEL-CQYVIIGHSERRAYFGETGQVVNQKIKAALQAGLLPIVCVGEKPEENENGQTRQVLETQLKEALDGLN--L-SCIIIAYEPIWAI-GTGKAATASEANSAIGYIRRVLGDTLGNAAAQTSPILYGGSVNEKNITEILSQTNIDGALVGGASLKAESFVSICRQAAVIQ-NKH ->A0QHY3 ----------------------MSRKPLIAGNWKMNLNHFEAIALVQKIAFAL-PDKYYDKVDVTVLPPFTDLRSVQTLVDGDKLRLSYGAQDLSQHDSGAYTGDISGAFLAKLGCTFVVVGHSERRTYHNEDDALVAAKAAAALKHELTPIICIGEHLEVREAGNHVIHCEEQLRGSLAGLSAEQIGKVVIAYEPVWAI-GTGRVASASDAQEVCAAIRKELASLASAQIADSVRVLYGGSVNAKNVGELIAQDDIDGGLVGGASLDGEQFATLAAIAAGGP-L-P ->P9WG42 ----------------------MSRKPLIAGNWKMNLNHYEAIALVQKIAFSL-PDKYYDRVDVAVIPPFTDLRSVQTLVDGDKLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAI-GTGRVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGGASLDGEHFATLAAIAAGGP-L-P ->Q3KM32 -MFTDKETHRKPFPTWAHLLHSEPSKQFVFGNWKMNKTLTEAQTFLKSFISSDIL--SNPQIITGIIPPFTLLSACQQAVS--DSPIFLGAQTTHEADSGAFTGEISAPMLKDIGVDFVLIGHSERRHIFHEQNPVLAEKAAAAIHSGMIPVLCIGETLEEQESGATQDILLNQLTIGLSKLPEQA--SFILAYEPVWAI-GTGKVAHPDLVQETHAFCRKTIASLFSKDIAERTPILYGGSVKADDARSLSLCPDVNGLLVGGASLSSENFLSIIQQVDIP----- ->A0R756 -------------MPDARA-L-GAAQLWIGTSWKMNKGLAESRGYARELAEYV-AAKPPAGVQPFIIPSFTALTTVRDALGD-DSPVLLGVQNAHWEDHGAWTGEVSVAQAKDAGAQIVEIGHSERREHFGETVETTRLKVAAALHHGLVPLLCIGESAENKQAGESSRFILEQAAGALEGLTDEHLARVLIAYEPIWAIGENGRPATVEELRQPFDDLAREYG-----CR--TMGLLYGGSVNTDNAEDLLGIDHVTGLFIGRAAWQLPGYVRILEMAAAHPKAKA ->Q8Z2Y2 -----------------------MRHPLVMGNWKLNGSRHMVNELVANLRKEL-T--GVAGCDVAIAPPEMYIDLAKRAAA--GSHIMLGAQNVDLNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDTVLKTQGAAAFEGAVIAYEPVWAI-GTGKSATPAQAQAVHKFIRDHIAKA-DAKIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFAVIVKAAEAAK-Q-A ->Q8ZJK9 -----------------------MRHPLVMGNWKLNGSTHMVNELIAGLRKEL-S--TVDGCGVAIAPPAIYLNQAKHELA--GSRIALGAQNVDVNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHQESDELIAKKFGVLKEIGLIPVLCIGESEAENEAGQTEAVCAKQLDAVLNTLGVKAFEGAVIAYEPIWAI-GTGKSATPAQAQAVHKFIRDHIAKQ-DAAVAAQVIIQYGGSVNDKNAAELFTQPDIDGALVGGASLKADAFAVIVKAAAKAK-K-A diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/seqs/converted_aligned_Subset1.fasta b/toy_example/results/toy_example_2023_12_07_20_58_09/seqs/converted_aligned_Subset1.fasta deleted file mode 100644 index 7cfbc44..0000000 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/seqs/converted_aligned_Subset1.fasta +++ /dev/null @@ -1,6 +0,0 @@ ->A1RUV7 -MKFPILIINLKAYGEAAGKKALEIAKAAEKVAKELGVNIAVAPNHLELALVAQSVEIPVYAQGADVETPGAYTAHIAVDNIKAVGASGLILNHSEAPLALNQLSKLAARAKSIGLDVVICAPDPVTSLAAAALGPHAVAVEPPELIGTGKAVSKYKPETIIETVRLVTKHFPNVVVITGAGIETGEDVEAALKLGTKGVLLASAAVKAKDHYQKIFELAKPLTVAAEP--P ->Q97VM8 -MKPPIIIINFKAYENSFGDKAVNLGKKIEKISKEYSVEIILSTPATMIYRMSQEVDLPIYAEHVDPVPLGAFTGAILPEMVKDAGAKGTLINHSERRLRADEIDDVLKRTKKLGLKSILCVDRYELVYPFSLLKPDAILIEPPELIGTGVSVSKAKPEVITRAVDEIRK-SEGIYLIAGAGITTGEDVYKALKLGAHGIGVASAVMKAKEPEKVVEDFITSALRAISS--- ->Q4JCD8 -MKPPVILINYKAYENSYGKKSIEITKKIEKVSKEYGTEIIVSVPATMIHRISEESELTVFAQHVDSGEQGARTGAILPEMIKDAGARGSLLNHSERRIRLDEMAESLERIRVLNLESVVCVDRYELVLPVALLRPNAVLIEPPELIGTGIPVSKAKPEAITKAVEEIKK-TKDVYLLAGAGITTGEDVFKAIELGADGIGAASAVMKAKEPEKVVEDFVKNAIKAMEKRGE diff --git a/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/dssp_merged_magicMSA_alignment.fasta b/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/dssp_merged_magicMSA_alignment.fasta new file mode 100644 index 0000000..d5dc0fe --- /dev/null +++ b/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/dssp_merged_magicMSA_alignment.fasta @@ -0,0 +1,22 @@ +>A1RUV7 +----------------------XXSSEEEEEXTTXGGGSTHHHHHHHHHHHHHH-H-H-H-T-XEEEEEXXTTTHHHHHTTX-----SSXBEESXXSBSSXSSXTTXXBHHHHHHTTXXEEEESXTTSX----XXHHHHHHHHHHHHHTTXEEEEEESSH---------H--HH--HH-HHT------TXXSEEEEXXGGGTT-SSXXHHHHXH-HHHHHHHHHHHHH-----XTTSEEEEESSXXSHHHHHHHHHT-TXSEEEEXHHHHTXSSHHHHHHHHHTHHHHTT--SX--X +>P72484 +---------------------XXXXXEEEEEXXSX--XXHHHHHHHHHHHTTSS-X-X-T-TTXEEEEEEXGGGHHHHHHHTT--TSSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHTXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHHHXEEEEXXGGGTT-SSXXXXHHHHHHHHHHHHHHHHHHHXHHHHHHSEEEEXSSXXTT-THHHHHTSSSXXEEEESGGGS-S--H-HHHHHTTGG-GX--------- +>A5FRB6 +----------------------XXXXEEEEEXXSX--XXHHHHHHHHHHHHHHH-H-T-X-XSSEEEEEXXHHHHHHHHHHTT--TXSXEEEESXXXSSSSSSXTTXXXHHHHTTT-XSEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHTTXX--X-SXXEEEEXXGGGTT-SSXXXXHHHHHHHHHHHHHHHHHHHXHHHHHHSXEEEXSSXXTT-THHHHHTSTTXXEEEEXGGGG-S--H-HHHHHHHHHHHHHH--TT--X +>A0QHY3 +---------------------XXXXXEEEEEXXSX--XXHHHHHHHHHHHHHHS-XGG-GGGTXEEEEEXXGGGHHHHHHHHHHHTXSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHTTXEEEEXXGGGSS-SSXXXXHHHHHHHHHHHHHHHHHHSXHHHHTTSEEEEXSXXXTT-THHHHHTSTTXXEEEEXGGGG-S--H-HHHHHHHHHHTTXX--X---X +>P9WG42 +---------------------XXXXXEEEEEXXSX--XXHHHHHHHHHHHHHHS-XGG-GGGTXEEEEEXXGGGHHHHHHHHHHHTXSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHTTXEEEEXXGGGTT-SSXXXXHHHHHHHHHHHHHHHHHHTXHHHHTTSEEEEXSXXXTT-THHHHHTSTTXXEEEEXGGGG-S--H-HHHHHHHHHHTTSS--X---X +>Q3KM32 +XXXXXXXXXXXXXXHHHHHTSXTTXEEEEEEXXSX--XXHHHHHHHHHHHTTXGGG-G-X-TTEEEEEEXXGGGHHHHHHHHT--TSSXEEEESXXBSSSSSSXTTXXBHHHHHHHTXXEEEESXHHHHHTSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTSXTTX--XXEEEEXXGGGSS-SSXXXXHHHHHHHHHHHHHHHHHHSXHHHHHHSXEEEXSXXXHH-HHHHHHTSTTXXEEEESGGGG-S--H-HHHHHHHHHSXXX-------- +>A0R756 +------------XXXTTX-X-XSXXEEEEEEXTTX--XXHHHHHHHHHHHHHHH-HHSXX-TTEEEEEEXXGGGHHHHHHHHXT-TXSSEEEESXXBSSSSSSXTTXXBHHHHHHTTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHTTXXHHHHTTXEEEEXXGGGSSTTXXXXXHHHHHHHHHHHIIIII-----TT--SSEEEEEESXXTT-THHHHHHSTTXXEEEESHHHH-S--H-HHHHHHHHHHHHSGGGG---X +>Q8Z2Y2 +----------------------XXXXEEEEEXXSX--XXHHHHHHHHHHHHHHT-T-T-X-XSSEEEEEXXGGGHHHHHHHHT--TSXEEEEESXXXSXSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHHHHXGGGGTTXEEEEXXGGGSS-SSXXXXHHHHHHHHHHHHHHHHTT-XHHHHHHXEEEEXSXXXTT-THHHHHTSTTXXEEEESGGGG-S--H-HHHHHHHHHHHHHH--H---X +>Q8ZJK9 +----------------------XXXXEEEEEXXSX--XXHHHHHHHHHHHHHHH-T-T-X-XSSEEEEEXXGGGHHHHHHHTT--TSSEEEEESXXXSXSSSSXTTXXXHHHHHHHTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHHTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHHHHXGGGGTTXEEEEXXGGGSS-SSXXXXHHHHHHHHHHHHHHHHTT-XHHHHHHXEEEEXSXXXTT-THHHHHTSTTXXEEEESGGGG-S--H-HHHHHHHHHHHHHT--T---X +>Q97VM8 +----------------------XXSSEEEEEXTTXTTSSHHHHHHHHHHHHHHH-H-H-H-T-XXEEEEEXGGGHHHHHHHX-----SSXEEESXXXXXXSSSXTTXXXHHHHHHTTXSEEEESXTTSX----XXHHHHHHHHHHHHHTTXEEEEEESSG---------G--GH--HH-HHT------TXXSEEEEXXGGGTT-SSXXHHHHXH-HHHHHHHHHHTT------SSSXEEEEXSSXXSHHHHHHHHHT-TXSEEEESHHHHTXSSHHHHHHHHHHHHHHHH--X---X +>Q4JCD8 +----------------------XXSSEEEEEXXSXGGGSHHHHHHHHHHHHHHH-H-H-T-T-XXEEEEEXGGGHHHHHHHX-----XSEEEESXXXXSXSSSXTTXXXHHHHHHTTXXEEEESXTTSX----XXHHHHHHHHHHHHHTTXEEEEEESSG---------G--GH--HH-HHT------TXXSEEEEXXGGGTT-SSXXHHHHXH-HHHHHHHHHHTT------SSSXEEEEXSSXXSHHHHHHHHHT-TXSEEEESHHHHTXSXHHHHHHHHHHHHHHHH--HHHTX diff --git a/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/dssp_squeezed_merged_magicMSA_alignment.fasta b/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/dssp_squeezed_merged_magicMSA_alignment.fasta new file mode 100644 index 0000000..34cc7d1 --- /dev/null +++ b/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/dssp_squeezed_merged_magicMSA_alignment.fasta @@ -0,0 +1,22 @@ +>A1RUV7 +----------------------XXSSEEEEEXTTXGGGSTHHHHHHHHHHHHHHHH---HTXEEEEEXXTTTHHHHHTTX-----SSXBEESXXSBSSXSSXTTXXBHHHHHHTTXXEEEESXTT----SXXXHHHHHHHHHHHHHTTXEEEEEESSHHHHH--------------------HHHTTXXSEEEEXXGGGTTSSXX--HHHHXHHHHHHHHHHHHHHX-----TTSEEEEESSXXSHHHHHHHHHT-TXSEEEEXHHHHTXSSHHHHHHHHHTHHHHTTSXX-- +>P72484 +---------------------XXXXXEEEEEXXS--XXXHHHHHHHHHHHTTSSXX--TTTXEEEEEEXGGGHHHHHHHTTT--SSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHTXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHHHXEEEEXXGGGTTSSXX-XXHHHHHHHHHHHHHHHHHHHXHHHHHHSEEEEXSSX-XTTTHHHHHTSSSXXEEEESGGGSS----HHHHHHTTGGGX-------- +>A5FRB6 +----------------------XXXXEEEEEXXS--XXXHHHHHHHHHHHHHHHHT--XXSSEEEEEXXHHHHHHHHHHTTT--XSXEEEESXXXSSSSSSXTTXXXHHHHTTT-XSEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHH---HHHHHHHHTTXXXSXXEEEEXXGGGTTSSXX-XXHHHHHHHHHHHHHHHHHHHXHHHHHHSXEEEXSSX-XTTTHHHHHTSTTXXEEEEXGGGGS----HHHHHHHHHHHHHHHTTX-- +>A0QHY3 +---------------------XXXXXEEEEEXXS--XXXHHHHHHHHHHHHHHSXGGGGGTXEEEEEXXGGGHHHHHHHHHHHTXSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHTTXEEEEXXGGGSSSSXX-XXHHHHHHHHHHHHHHHHHHSXHHHHTTSEEEEXSXX-XTTTHHHHHTSTTXXEEEEXGGGGS----HHHHHHHHHHHTTXXXX--- +>P9WG42 +---------------------XXXXXEEEEEXXS--XXXHHHHHHHHHHHHHHSXGGGGGTXEEEEEXXGGGHHHHHHHHHHHTXSXEEEESXXXSSSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHHXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHTTTXXHHHHTTXEEEEXXGGGTTSSXX-XXHHHHHHHHHHHHHHHHHHTXHHHHTTSEEEEXSXX-XTTTHHHHHTSTTXXEEEEXGGGGS----HHHHHHHHHHHTTSSXX--- +>Q3KM32 +XXXXXXXXXXXXXXHHHHHTSXTTXEEEEEEXXS--XXXHHHHHHHHHHHTTXGGGG-XTTEEEEEEXXGGGHHHHHHHHTT--SSXEEEESXXBSSSSSSXTTXXBHHHHHHHTXXEEEESXHHHHHTSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHH--HHHHHHHTTTSXTTXXXEEEEXXGGGSSSSXX-XXHHHHHHHHHHHHHHHHHHSXHHHHHHSXEEEXSXX-XHHHHHHHHTSTTXXEEEESGGGGS----HHHHHHHHHHSXXX------ +>A0R756 +--------------XXXTTXXXSXXEEEEEEXTT--XXXHHHHHHHHHHHHHHHHHSXXTTEEEEEEXXGGGHHHHHHHHXT-TXSSEEEESXXBSSSSSSXTTXXBHHHHHHTTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHTTXXHHHHTTXEEEEXXGGGSSTTXXXXXHHHHHHHHHHHIIIIITT-------SSEEEEEESX-XTTTHHHHHHSTTXXEEEESHHHHS----HHHHHHHHHHHHHSGGGGX- +>Q8Z2Y2 +----------------------XXXXEEEEEXXS--XXXHHHHHHHHHHHHHHTTT--XXSSEEEEEXXGGGHHHHHHHHTT--SXEEEEESXXXSXSSSSXTTXXXHHHHHHTTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHTTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHHHHXGGGGTTXEEEEXXGGGSSSSXX-XXHHHHHHHHHHHHHHHHTTXHH-HHHHXEEEEXSXX-XTTTHHHHHTSTTXXEEEESGGGGS----HHHHHHHHHHHHHHHHX--- +>Q8ZJK9 +----------------------XXXXEEEEEXXS--XXXHHHHHHHHHHHHHHHTT--XXSSEEEEEXXGGGHHHHHHHTTT--SSEEEEESXXXSXSSSSXTTXXXHHHHHHHTXXEEEESXHHHHHHSXXXHHHHHHHHHHHHHHTXEEEEEEXXXHHHHHTTXHHHHHHHHHHHHHHHHXGGGGTTXEEEEXXGGGSSSSXX-XXHHHHHHHHHHHHHHHHTTXHH-HHHHXEEEEXSXX-XTTTHHHHHTSTTXXEEEESGGGGS----HHHHHHHHHHHHHHTTX--- +>Q97VM8 +----------------------XXSSEEEEEXTTXTTSSHHHHHHHHHHHHHHHHH---HTXXEEEEEXGGGHHHHHHHX-----SSXEEESXXXXXXSSSXTTXXXHHHHHHTTXSEEEESXTT----SXXXHHHHHHHHHHHHHTTXEEEEEESSGGGHH--------------------HHHTTXXSEEEEXXGGGTTSSXX--HHHHXHHHHHHHHHHHTTS------SSXEEEEXSSXXSHHHHHHHHHT-TXSEEEESHHHHTXSSHHHHHHHHHHHHHHHHXX--- +>Q4JCD8 +----------------------XXSSEEEEEXXSXGGGSHHHHHHHHHHHHHHHHH---TTXXEEEEEXGGGHHHHHHHX-----XSEEEESXXXXSXSSSXTTXXXHHHHHHTTXXEEEESXTT----SXXXHHHHHHHHHHHHHTTXEEEEEESSGGGHH--------------------HHHTTXXSEEEEXXGGGTTSSXX--HHHHXHHHHHHHHHHHTTS------SSXEEEEXSSXXSHHHHHHHHHT-TXSEEEESHHHHTXSXHHHHHHHHHHHHHHHHHHHTX diff --git a/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/merged_magicMSA_alignment.fasta b/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/merged_magicMSA_alignment.fasta new file mode 100644 index 0000000..ecdcf47 --- /dev/null +++ b/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/merged_magicMSA_alignment.fasta @@ -0,0 +1,22 @@ +>A1RUV7 +----------------------MKFPILIINLKAYGEAAGKKALEIAKAAEKVA-K-E-L-G-VNIAVAPNHLELALVAQSV-----EIPVYAQGADVETPGAYTAHIAVDNIKAVGASGLILNHSEAP----LALNQLSKLAARAKSIGLDVVICAPDP---------V--TS--LA-AAA------LGPHAVAVEPPELIG-TGKAVSKYKP-ETIIETVRLVTKH-----FPNVVVITGAGIETGEDVEAALKL-GTKGVLLASAAVKAKDHYQKIFELAKPLTVAA--EP--P +>P72484 +---------------------MSRKPIIAGNWKMN--KTAAEAREFIDAVKNNI-P-S-N-NLVDTVIGSPALFLEGMKKGVK--GTELQVAAQNCYWEDFGAFTGETSPAALAALGVDYVIIGHSERRDYFHETDQEINKKAHAIFKHKMTPILCCGESLETYEAGKTAEWIEGQITADLKGLSAEQVSSMVIAYEPIWAIG-TGKSADANIADDICGVVRATVEKLYGKEVAQAVRIQYGGSVKPE-NVAEYMAKENVDGALVGGASL-Q--A-DSFLALLDF-VK--------- +>A5FRB6 +----------------------MRQIIIAGNWKMN--TTLSEACTLVQSMKCEL-E-R-I-EGIEKIICPPFISLYPIKTMLE--NSSIKLGAQNLFYQEKGAYTGEISPLMLKEL-CQYVIIGHSERRAYFGETGQVVNQKIKAALQAGLLPIVCVGEKPEENENGQTRQVLETQLKEALDGLN--L-SCIIIAYEPIWAIG-TGKAATASEANSAIGYIRRVLGDTLGNAAAQTSPILYGGSVNEK-NITEILSQTNIDGALVGGASL-K--A-ESFVSICRQAAVIQ--NK--H +>A0QHY3 +---------------------MSRKPLIAGNWKMN--LNHFEAIALVQKIAFAL-PDK-YYDKVDVTVLPPFTDLRSVQTLVDGDKLRLSYGAQDLSQHDSGAYTGDISGAFLAKLGCTFVVVGHSERRTYHNEDDALVAAKAAAALKHELTPIICIGEHLEVREAGNHVIHCEEQLRGSLAGLSAEQIGKVVIAYEPVWAIG-TGRVASASDAQEVCAAIRKELASLASAQIADSVRVLYGGSVNAK-NVGELIAQDDIDGGLVGGASL-D--G-EQFATLAAIAAGGP--L---P +>P9WG42 +---------------------MSRKPLIAGNWKMN--LNHYEAIALVQKIAFSL-PDK-YYDRVDVAVIPPFTDLRSVQTLVDGDKLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIG-TGRVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAK-NVGDIVAQDDVDGGLVGGASL-D--G-EHFATLAAIAAGGP--L---P +>Q3KM32 +MFTDKETHRKPFPTWAHLLHSEPSKQFVFGNWKMN--KTLTEAQTFLKSFISSDIL-S-N-PQIITGIIPPFTLLSACQQAVS--DSPIFLGAQTTHEADSGAFTGEISAPMLKDIGVDFVLIGHSERRHIFHEQNPVLAEKAAAAIHSGMIPVLCIGETLEEQESGATQDILLNQLTIGLSKLPEQA--SFILAYEPVWAIG-TGKVAHPDLVQETHAFCRKTIASLFSKDIAERTPILYGGSVKAD-DARSLSLCPDVNGLLVGGASL-S--S-ENFLSIIQQVDIP-------- +>A0R756 +------------MPDARA-L-GAAQLWIGTSWKMN--KGLAESRGYARELAEYV-AAKPP-AGVQPFIIPSFTALTTVRDALGD-DSPVLLGVQNAHWEDHGAWTGEVSVAQAKDAGAQIVEIGHSERREHFGETVETTRLKVAAALHHGLVPLLCIGESAENKQAGESSRFILEQAAGALEGLTDEHLARVLIAYEPIWAIGENGRPATVEELRQPFDDLAREYG-----CR--TMGLLYGGSVNTD-NAEDLLGIDHVTGLFIGRAAW-Q--L-PGYVRILEMAAAHPKAK---A +>Q8Z2Y2 +----------------------MRHPLVMGNWKLN--GSRHMVNELVANLRKEL-T-G-V-AGCDVAIAPPEMYIDLAKRAAA--GSHIMLGAQNVDLNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDTVLKTQGAAAFEGAVIAYEPVWAIG-TGKSATPAQAQAVHKFIRDHIAKA-DAKIAEQVIIQYGGSVNAS-NAAELFAQPDIDGALVGGASL-K--A-DAFAVIVKAAEAAK--Q---A +>Q8ZJK9 +----------------------MRHPLVMGNWKLN--GSTHMVNELIAGLRKEL-S-T-V-DGCGVAIAPPAIYLNQAKHELA--GSRIALGAQNVDVNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHQESDELIAKKFGVLKEIGLIPVLCIGESEAENEAGQTEAVCAKQLDAVLNTLGVKAFEGAVIAYEPIWAIG-TGKSATPAQAQAVHKFIRDHIAKQ-DAAVAAQVIIQYGGSVNDK-NAAELFTQPDIDGALVGGASL-K--A-DAFAVIVKAAAKAK--K---A +>Q97VM8 +----------------------MKPPIIIINFKAYENSFGDKAVNLGKKIEKIS-K-E-Y-S-VEIILSTPATMIYRMSQEV-----DLPIYAEHVDPVPLGAFTGAILPEMVKDAGAKGTLINHSERR----LRADEIDDVLKRTKKLGLKSILCVDRY---------E--LV--YP-FSL------LKPDAILIEPPELIG-TGVSVSKAKP-EVITRAVDEIRK------SEGIYLIAGAGITTGEDVYKALKL-GAHGIGVASAVMKAKEPEKVVEDFITSALRAI--S---S +>Q4JCD8 +----------------------MKPPVILINYKAYENSYGKKSIEITKKIEKVS-K-E-Y-G-TEIIVSVPATMIHRISEES-----ELTVFAQHVDSGEQGARTGAILPEMIKDAGARGSLLNHSERR----IRLDEMAESLERIRVLNLESVVCVDRY---------E--LV--LP-VAL------LRPNAVLIEPPELIG-TGIPVSKAKP-EAITKAVEEIKK------TKDVYLLAGAGITTGEDVFKAIEL-GADGIGAASAVMKAKEPEKVVEDFVKNAIKAM--EKRGE diff --git a/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/squeezed_merged_magicMSA_alignment.fasta b/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/squeezed_merged_magicMSA_alignment.fasta new file mode 100644 index 0000000..f46d690 --- /dev/null +++ b/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/squeezed_merged_magicMSA_alignment.fasta @@ -0,0 +1,22 @@ +>A1RUV7 +----------------------MKFPILIINLKAYGEAAGKKALEIAKAAEKVAKE---LGVNIAVAPNHLELALVAQSV-----EIPVYAQGADVETPGAYTAHIAVDNIKAVGASGLILNHSE----APLALNQLSKLAARAKSIGLDVVICAPDPVTSL--------------------AAAALGPHAVAVEPPELIGTGKA--VSKYKPETIIETVRLVTKHF-----PNVVVITGAGIETGEDVEAALKL-GTKGVLLASAAVKAKDHYQKIFELAKPLTVAAEPP-- +>P72484 +---------------------MSRKPIIAGNWKM--NKTAAEAREFIDAVKNNIPS--NNLVDTVIGSPALFLEGMKKGVKG--TELQVAAQNCYWEDFGAFTGETSPAALAALGVDYVIIGHSERRDYFHETDQEINKKAHAIFKHKMTPILCCGESLETYEAGKTAEWIEGQITADLKGLSAEQVSSMVIAYEPIWAIGTGKS-ADANIADDICGVVRATVEKLYGKEVAQAVRIQYGGSV-KPENVAEYMAKENVDGALVGGASLQ----ADSFLALLDFVK-------- +>A5FRB6 +----------------------MRQIIIAGNWKM--NTTLSEACTLVQSMKCELER--IEGIEKIICPPFISLYPIKTMLEN--SSIKLGAQNLFYQEKGAYTGEISPLMLKEL-CQYVIIGHSERRAYFGETGQVVNQKIKAALQAGLLPIVCVGEKPEENENGQTRQVL---ETQLKEALDGLNLSCIIIAYEPIWAIGTGKA-ATASEANSAIGYIRRVLGDTLGNAAAQTSPILYGGSV-NEKNITEILSQTNIDGALVGGASLK----AESFVSICRQAAVIQNKH-- +>A0QHY3 +---------------------MSRKPLIAGNWKM--NLNHFEAIALVQKIAFALPDKYYDKVDVTVLPPFTDLRSVQTLVDGDKLRLSYGAQDLSQHDSGAYTGDISGAFLAKLGCTFVVVGHSERRTYHNEDDALVAAKAAAALKHELTPIICIGEHLEVREAGNHVIHCEEQLRGSLAGLSAEQIGKVVIAYEPVWAIGTGRV-ASASDAQEVCAAIRKELASLASAQIADSVRVLYGGSV-NAKNVGELIAQDDIDGGLVGGASLD----GEQFATLAAIAAGGPLP--- +>P9WG42 +---------------------MSRKPLIAGNWKM--NLNHYEAIALVQKIAFSLPDKYYDRVDVAVIPPFTDLRSVQTLVDGDKLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIGTGRV-ASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSV-NAKNVGDIVAQDDVDGGLVGGASLD----GEHFATLAAIAAGGPLP--- +>Q3KM32 +MFTDKETHRKPFPTWAHLLHSEPSKQFVFGNWKM--NKTLTEAQTFLKSFISSDILS-NPQIITGIIPPFTLLSACQQAVSD--SPIFLGAQTTHEADSGAFTGEISAPMLKDIGVDFVLIGHSERRHIFHEQNPVLAEKAAAAIHSGMIPVLCIGETLEEQESGATQDIL--LNQLTIGLSKLPEQASFILAYEPVWAIGTGKV-AHPDLVQETHAFCRKTIASLFSKDIAERTPILYGGSV-KADDARSLSLCPDVNGLLVGGASLS----SENFLSIIQQVDIP------ +>A0R756 +--------------MPDARALGAAQLWIGTSWKM--NKGLAESRGYARELAEYVAAKPPAGVQPFIIPSFTALTTVRDALGD-DSPVLLGVQNAHWEDHGAWTGEVSVAQAKDAGAQIVEIGHSERREHFGETVETTRLKVAAALHHGLVPLLCIGESAENKQAGESSRFILEQAAGALEGLTDEHLARVLIAYEPIWAIGENGRPATVEELRQPFDDLAREYGCR-------TMGLLYGGSV-NTDNAEDLLGIDHVTGLFIGRAAWQ----LPGYVRILEMAAAHPKAKA- +>Q8Z2Y2 +----------------------MRHPLVMGNWKL--NGSRHMVNELVANLRKELTG--VAGCDVAIAPPEMYIDLAKRAAAG--SHIMLGAQNVDLNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDTVLKTQGAAAFEGAVIAYEPVWAIGTGKS-ATPAQAQAVHKFIRDHIAKADAK-IAEQVIIQYGGSV-NASNAAELFAQPDIDGALVGGASLK----ADAFAVIVKAAEAAKQA--- +>Q8ZJK9 +----------------------MRHPLVMGNWKL--NGSTHMVNELIAGLRKELST--VDGCGVAIAPPAIYLNQAKHELAG--SRIALGAQNVDVNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHQESDELIAKKFGVLKEIGLIPVLCIGESEAENEAGQTEAVCAKQLDAVLNTLGVKAFEGAVIAYEPIWAIGTGKS-ATPAQAQAVHKFIRDHIAKQDAA-VAAQVIIQYGGSV-NDKNAAELFTQPDIDGALVGGASLK----ADAFAVIVKAAAKAKKA--- +>Q97VM8 +----------------------MKPPIIIINFKAYENSFGDKAVNLGKKIEKISKE---YSVEIILSTPATMIYRMSQEV-----DLPIYAEHVDPVPLGAFTGAILPEMVKDAGAKGTLINHSE----RRLRADEIDDVLKRTKKLGLKSILCVDRYELVY--------------------PFSLLKPDAILIEPPELIGTGVS--VSKAKPEVITRAVDEIRKS------EGIYLIAGAGITTGEDVYKALKL-GAHGIGVASAVMKAKEPEKVVEDFITSALRAISS--- +>Q4JCD8 +----------------------MKPPVILINYKAYENSYGKKSIEITKKIEKVSKE---YGTEIIVSVPATMIHRISEES-----ELTVFAQHVDSGEQGARTGAILPEMIKDAGARGSLLNHSE----RRIRLDEMAESLERIRVLNLESVVCVDRYELVL--------------------PVALLRPNAVLIEPPELIGTGIP--VSKAKPEAITKAVEEIKKT------KDVYLLAGAGITTGEDVFKAIEL-GADGIGAASAVMKAKEPEKVVEDFVKNAIKAMEKRGE diff --git a/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/t-coffee/aligned_Subset0.aln b/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/t-coffee/aligned_Subset0.aln new file mode 100644 index 0000000..c8dca59 --- /dev/null +++ b/toy_example/results/toy_example_2024_03_21_16_08_33_test/msas/t-coffee/aligned_Subset0.aln @@ -0,0 +1,82 @@ +CLUSTAL FORMAT for T-COFFEE Version_13.45.61.3c310a9 [http://www.tcoffee.org] [MODE: 3dcoffee ], CPU=1.23 sec, SCORE=92, Nseq=11, Len=297 + +A1RUV7 ----------------------MKFPILIINLKAYGEAAGKKALEIAKAA +P72484 ---------------------MSRKPIIAGNWKMN--KTAAEAREFIDAV +A5FRB6 ----------------------MRQIIIAGNWKMN--TTLSEACTLVQSM +A0QHY3 ---------------------MSRKPLIAGNWKMN--LNHFEAIALVQKI +P9WG42 ---------------------MSRKPLIAGNWKMN--LNHYEAIALVQKI +Q3KM32 MFTDKETHRKPFPTWAHLLHSEPSKQFVFGNWKMN--KTLTEAQTFLKSF +A0R756 ------------MPDARA-L-GAAQLWIGTSWKMN--KGLAESRGYAREL +Q8Z2Y2 ----------------------MRHPLVMGNWKLN--GSRHMVNELVANL +Q8ZJK9 ----------------------MRHPLVMGNWKLN--GSTHMVNELIAGL +Q97VM8 ----------------------MKPPIIIINFKAYENSFGDKAVNLGKKI +Q4JCD8 ----------------------MKPPVILINYKAYENSYGKKSIEITKKI + : . * + +A1RUV7 EKVA-K-E-L-G-VNIAVAPNHLELALVAQSV-----EIPVYAQGADVET +P72484 KNNI-P-S-N-NLVDTVIGSPALFLEGMKKGVK--GTELQVAAQNCYWED +A5FRB6 KCEL-E-R-I-EGIEKIICPPFISLYPIKTMLE--NSSIKLGAQNLFYQE +A0QHY3 AFAL-PDK-YYDKVDVTVLPPFTDLRSVQTLVDGDKLRLSYGAQDLSQHD +P9WG42 AFSL-PDK-YYDRVDVAVIPPFTDLRSVQTLVDGDKLRLTYGAQDLSPHD +Q3KM32 ISSDIL-S-N-PQIITGIIPPFTLLSACQQAVS--DSPIFLGAQTTHEAD +A0R756 AEYV-AAKPP-AGVQPFIIPSFTALTTVRDALGD-DSPVLLGVQNAHWED +Q8Z2Y2 RKEL-T-G-V-AGCDVAIAPPEMYIDLAKRAAA--GSHIMLGAQNVDLNL +Q8ZJK9 RKEL-S-T-V-DGCGVAIAPPAIYLNQAKHELA--GSRIALGAQNVDVNL +Q97VM8 EKIS-K-E-Y-S-VEIILSTPATMIYRMSQEV-----DLPIYAEHVDPVP +Q4JCD8 EKVS-K-E-Y-G-TEIIVSVPATMIHRISEES-----ELTVFAQHVDSGE + : : : .: + +A1RUV7 PGAYTAHIAVDNIKAVGASGLILNHSEAP----LALNQLSKLAARAKSIG +P72484 FGAFTGETSPAALAALGVDYVIIGHSERRDYFHETDQEINKKAHAIFKHK +A5FRB6 KGAYTGEISPLMLKEL-CQYVIIGHSERRAYFGETGQVVNQKIKAALQAG +A0QHY3 SGAYTGDISGAFLAKLGCTFVVVGHSERRTYHNEDDALVAAKAAAALKHE +P9WG42 SGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATALKHG +Q3KM32 SGAFTGEISAPMLKDIGVDFVLIGHSERRHIFHEQNPVLAEKAAAAIHSG +A0R756 HGAWTGEVSVAQAKDAGAQIVEIGHSERREHFGETVETTRLKVAAALHHG +Q8Z2Y2 SGAFTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG +Q8ZJK9 SGAFTGETSAEMLKDIGAQYIIIGHSERRTYHQESDELIAKKFGVLKEIG +Q97VM8 LGAFTGAILPEMVKDAGAKGTLINHSERR----LRADEIDDVLKRTKKLG +Q4JCD8 QGARTGAILPEMIKDAGARGSLLNHSERR----IRLDEMAESLERIRVLN + ** *. :.*** + +A1RUV7 LDVVICAPDP---------V--TS--LA-AAA------LGPHAVAVEPPE +P72484 MTPILCCGESLETYEAGKTAEWIEGQITADLKGLSAEQVSSMVIAYEPIW +A5FRB6 LLPIVCVGEKPEENENGQTRQVLETQLKEALDGLN--L-SCIIIAYEPIW +A0QHY3 LTPIICIGEHLEVREAGNHVIHCEEQLRGSLAGLSAEQIGKVVIAYEPVW +P9WG42 LTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVW +Q3KM32 MIPVLCIGETLEEQESGATQDILLNQLTIGLSKLPEQA--SFILAYEPVW +A0R756 LVPLLCIGESAENKQAGESSRFILEQAAGALEGLTDEHLARVLIAYEPIW +Q8Z2Y2 LTPVLCIGETEAENEAGKTEEVCARQIDTVLKTQGAAAFEGAVIAYEPVW +Q8ZJK9 LIPVLCIGESEAENEAGQTEAVCAKQLDAVLNTLGVKAFEGAVIAYEPIW +Q97VM8 LKSILCVDRY---------E--LV--YP-FSL------LKPDAILIEPPE +Q4JCD8 LESVVCVDRY---------E--LV--LP-VAL------LRPNAVLIEPPE + : ::* : ** + +A1RUV7 LIG-TGKAVSKYKP-ETIIETVRLVTKH-----FPNVVVITGAGIETGED +P72484 AIG-TGKSADANIADDICGVVRATVEKLYGKEVAQAVRIQYGGSVKPE-N +A5FRB6 AIG-TGKAATASEANSAIGYIRRVLGDTLGNAAAQTSPILYGGSVNEK-N +A0QHY3 AIG-TGRVASASDAQEVCAAIRKELASLASAQIADSVRVLYGGSVNAK-N +P9WG42 AIG-TGRVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAK-N +Q3KM32 AIG-TGKVAHPDLVQETHAFCRKTIASLFSKDIAERTPILYGGSVKAD-D +A0R756 AIGENGRPATVEELRQPFDDLAREYG-----CR--TMGLLYGGSVNTD-N +Q8Z2Y2 AIG-TGKSATPAQAQAVHKFIRDHIAKA-DAKIAEQVIIQYGGSVNAS-N +Q8ZJK9 AIG-TGKSATPAQAQAVHKFIRDHIAKQ-DAAVAAQVIIQYGGSVNDK-N +Q97VM8 LIG-TGVSVSKAKP-EVITRAVDEIRK------SEGIYLIAGAGITTGED +Q4JCD8 LIG-TGIPVSKAKP-EAITKAVEEIKK------TKDVYLLAGAGITTGED + ** .* . : *..: : + +A1RUV7 VEAALKL-GTKGVLLASAAVKAKDHYQKIFELAKPLTVAA--EP--P +P72484 VAEYMAKENVDGALVGGASL-Q--A-DSFLALLDF-VK--------- +A5FRB6 ITEILSQTNIDGALVGGASL-K--A-ESFVSICRQAAVIQ--NK--H +A0QHY3 VGELIAQDDIDGGLVGGASL-D--G-EQFATLAAIAAGGP--L---P +P9WG42 VGDIVAQDDVDGGLVGGASL-D--G-EHFATLAAIAAGGP--L---P +Q3KM32 ARSLSLCPDVNGLLVGGASL-S--S-ENFLSIIQQVDIP-------- +A0R756 AEDLLGIDHVTGLFIGRAAW-Q--L-PGYVRILEMAAAHPKAK---A +Q8Z2Y2 AAELFAQPDIDGALVGGASL-K--A-DAFAVIVKAAEAAK--Q---A +Q8ZJK9 AAELFTQPDIDGALVGGASL-K--A-DAFAVIVKAAAKAK--K---A +Q97VM8 VYKALKL-GAHGIGVASAVMKAKEPEKVVEDFITSALRAI--S---S +Q4JCD8 VFKAIEL-GADGIGAASAVMKAKEPEKVVEDFVKNAIKAM--EKRGE + * . * : + + + diff --git a/toy_example/results/toy_example_2023_12_07_20_58_09/nextflow_report_finalMSA.html b/toy_example/results/toy_example_2024_03_21_16_08_33_test/nextflow_report_magicMSA.html similarity index 97% rename from toy_example/results/toy_example_2023_12_07_20_58_09/nextflow_report_finalMSA.html rename to toy_example/results/toy_example_2024_03_21_16_08_33_test/nextflow_report_magicMSA.html index fdd8965..aa1e728 100644 --- a/toy_example/results/toy_example_2023_12_07_20_58_09/nextflow_report_finalMSA.html +++ b/toy_example/results/toy_example_2024_03_21_16_08_33_test/nextflow_report_magicMSA.html @@ -18,11 +18,11 @@ - + - [romantic_carlsson] Nextflow Workflow Report + [intergalactic_lovelace] Nextflow Workflow Report