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zavolan_group
pipelines
ZARP
Commits
c3fffb6c
Commit
c3fffb6c
authored
5 years ago
by
BIOPZ-Bak Maciej
Browse files
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updated DAG and rulegraph
parent
65f265fb
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1 merge request
!43
add TIN score merge and plot steps
Pipeline
#10459
passed
5 years ago
Stage: test
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images/dag_test_workflow.svg
+411
-485
411 additions, 485 deletions
images/dag_test_workflow.svg
images/rule_graph.svg
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56 additions, 56 deletions
images/rule_graph.svg
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images/dag_test_workflow.svg
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c3fffb6c
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y=
"-231.5"
font-family=
"sans"
font-size=
"10.00"
>
generate_alfa_index
</text>
<!-- 26->12 -->
<g
id=
"edge33"
class=
"edge"
><title>
26
->
12
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1651.08,-215.876C1626.56,-204.799 1594.8,-190.457 1570.55,-179.504"
/>
<polygon
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"grey"
stroke=
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stroke-width=
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points=
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/>
</g>
<!-- 26->13 -->
<g
id=
"edge35"
class=
"edge"
><title>
26
->
13
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1684.06,-215.697C1681.83,-207.898 1679.15,-198.509 1676.67,-189.829"
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<polygon
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/>
</g>
<!-- 27->13 -->
<g
id=
"edge39"
class=
"edge"
>
<title>
27
->
13
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1848.99,-215.88C1828.65,-205.49 1802.7,-192.22 1781.87,-181.58"
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<polygon
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/>
</g>
<!-- 27->14 -->
<g
id=
"edge41"
class=
"edge"
>
<title>
27
->
14
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1880.03,-215.7C1878.93,-207.98 1877.6,-198.71 1876.37,-190.11"
/>
<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
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points=
"1879.82,-189.51 1874.94,-180.1 1872.89,-190.5 1879.82,-189.51"
/>
</g>
<!-- 28->14 -->
<g
id=
"edge40"
class=
"edge"
>
<title>
28
->
14
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1992.6,-215.88C1967.01,-204.61 1933.73,-189.96 1908.7,-178.94"
/>
<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
"2"
points=
"1910.1,-175.73 1899.54,-174.9 1907.28,-182.14 1910.1,-175.73"
/>
<g
id=
"edge34"
class=
"edge"
><title>
27
->
13
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1786.08,-215.876C1761.56,-204.799 1729.8,-190.457 1705.55,-179.504"
/>
<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
"2"
points=
"1706.87,-176.264 1696.32,-175.338 1703.99,-182.643 1706.87,-176.264"
/>
</g>
<!-- 28 -->
<g
id=
"node29"
class=
"node"
><title>
28
</title>
<path
fill=
"none"
stroke=
"#70d856"
stroke-width=
"2"
d=
"M994,-617C994,-617 726,-617 726,-617 720,-617 714,-611 714,-605 714,-605 714,-593 714,-593 714,-587 720,-581 726,-581 726,-581 994,-581 994,-581 1000,-581 1006,-587 1006,-593 1006,-593 1006,-605 1006,-605 1006,-611 1000,-617 994,-617"
/>
<text
text-anchor=
"middle"
x=
"860"
y=
"-602"
font-family=
"sans"
font-size=
"10.00"
>
pe_remove_adapters_cutadapt
</text>
<text
text-anchor=
"middle"
x=
"860"
y=
"-591"
font-family=
"sans"
font-size=
"10.00"
>
sample: synthetic_10_reads_paired_synthetic_10_reads_paired
</text>
</g>
<!-- 28->15 -->
<g
id=
"edge38"
class=
"edge"
><title>
28
->
15
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M860,-580.819C860,-572.422 860,-562.116 860,-552.686"
/>
<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
"2"
points=
"863.5,-552.558 860,-542.558 856.5,-552.558 863.5,-552.558"
/>
</g>
<!-- 29 -->
<g
id=
"node30"
class=
"node"
>
<title>
29
</title>
<path
fill=
"none"
stroke=
"#70d856"
stroke-width=
"2"
d=
"M1062,-617C1062,-617 761,-617 761,-617 755,-617 749,-611 749,-605 749,-605 749,-593 749,-593 749,-587 755,-581 761,-581 761,-581 1062,-581 1062,-581 1068,-581 1074,-587 1074,-593 1074,-593 1074,-605 1074,-605 1074,-611 1068,-617 1062,-617"
/>
<text
text-anchor=
"middle"
x=
"911.5"
y=
"-602"
font-family=
"sans"
font-size=
"10.00"
>
pe_remove_adapters_cutadapt
</text>
<text
text-anchor=
"middle"
x=
"911.5"
y=
"-591"
font-family=
"sans"
font-size=
"10.00"
>
sample: synthetic_10_reads_paired_synthetic_10_reads_paired
</text>
<g
id=
"node30"
class=
"node"
><title>
29
</title>
<path
fill=
"none"
stroke=
"#d85656"
stroke-width=
"2"
d=
"M1056.5,-324C1056.5,-324 955.5,-324 955.5,-324 949.5,-324 943.5,-318 943.5,-312 943.5,-312 943.5,-300 943.5,-300 943.5,-294 949.5,-288 955.5,-288 955.5,-288 1056.5,-288 1056.5,-288 1062.5,-288 1068.5,-294 1068.5,-300 1068.5,-300 1068.5,-312 1068.5,-312 1068.5,-318 1062.5,-324 1056.5,-324"
/>
<text
text-anchor=
"middle"
x=
"1006"
y=
"-309"
font-family=
"sans"
font-size=
"10.00"
>
extract_transcriptome
</text>
<text
text-anchor=
"middle"
x=
"1006"
y=
"-298"
font-family=
"sans"
font-size=
"10.00"
>
organism: homo_sapiens
</text>
</g>
<!-- 29->16 -->
<g
id=
"edge44"
class=
"edge"
>
<title>
29
->
16
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M911.5,-580.82C911.5,-572.42 911.5,-562.12 911.5,-552.69"
/>
<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
"2"
points=
"915,-552.56 911.5,-542.56 908,-552.56 915,-552.56"
/>
<g
id=
"edge39"
class=
"edge"
><title>
29
->
16
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1021.82,-287.697C1029.57,-279.22 1039.04,-268.864 1047.52,-259.583"
/>
<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
"2"
points=
"1050.2,-261.846 1054.36,-252.104 1045.03,-257.123 1050.2,-261.846"
/>
</g>
<!-- 30 -->
<g
id=
"node31"
class=
"node"
>
<title>
30
</title>
<path
fill=
"none"
stroke=
"#567bd8"
stroke-width=
"2"
d=
"M1128,-324C1128,-324 1013,-324 1013,-324 1007,-324 1001,-318 1001,-312 1001,-312 1001,-300 1001,-300 1001,-294 1007,-288 1013,-288 1013,-288 1128,-288 1128,-288 1134,-288 1140,-294 1140,-300 1140,-300 1140,-312 1140,-312 1140,-318 1134,-324 1128,-324"
/>
<text
text-anchor=
"middle"
x=
"1070.5"
y=
"-309"
font-family=
"sans"
font-size=
"10.00"
>
extract_transcriptome
</text>
<text
text-anchor=
"middle"
x=
"1070.5"
y=
"-298"
font-family=
"sans"
font-size=
"10.00"
>
organism: homo_sapiens
</text>
<!-- 33 -->
<g
id=
"node34"
class=
"node"
><title>
33
</title>
<path
fill=
"none"
stroke=
"#56d892"
stroke-width=
"2"
d=
"M985.5,-252C985.5,-252 900.5,-252 900.5,-252 894.5,-252 888.5,-246 888.5,-240 888.5,-240 888.5,-228 888.5,-228 888.5,-222 894.5,-216 900.5,-216 900.5,-216 985.5,-216 985.5,-216 991.5,-216 997.5,-222 997.5,-228 997.5,-228 997.5,-240 997.5,-240 997.5,-246 991.5,-252 985.5,-252"
/>
<text
text-anchor=
"middle"
x=
"943"
y=
"-237"
font-family=
"sans"
font-size=
"10.00"
>
create_index_salmon
</text>
<text
text-anchor=
"middle"
x=
"943"
y=
"-226"
font-family=
"sans"
font-size=
"10.00"
>
kmer: 31
</text>
</g>
<!-- 30->17 -->
<g
id=
"edge45"
class=
"edge"
>
<title>
30
->
17
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1053.2,-287.7C1044.64,-279.14 1034.16,-268.66 1024.8,-259.3"
/>
<polygon
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"grey"
stroke=
"grey"
stroke-width=
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points=
"1027.15,-256.7 1017.6,-252.1 1022.2,-261.65 1027.15,-256.7"
/>
<!-- 29->33 -->
<g
id=
"edge62"
class=
"edge"
><title>
29
->
33
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M990.427,-287.697C982.798,-279.22 973.477,-268.864 965.124,-259.583"
/>
<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
"2"
points=
"967.685,-257.196 958.394,-252.104 962.482,-261.879 967.685,-257.196"
/>
</g>
<!-- 33 -->
<g
id=
"node34"
class=
"node"
>
<title>
33
</title>
<path
fill=
"none"
stroke=
"#bed856"
stroke-width=
"2"
d=
"M1188,-252C1188,-252 1091,-252 1091,-252 1085,-252 1079,-246 1079,-240 1079,-240 1079,-228 1079,-228 1079,-222 1085,-216 1091,-216 1091,-216 1188,-216 1188,-216 1194,-216 1200,-222 1200,-228 1200,-228 1200,-240 1200,-240 1200,-246 1194,-252 1188,-252"
/>
<text
text-anchor=
"middle"
x=
"1139.5"
y=
"-237"
font-family=
"sans"
font-size=
"10.00"
>
create_index_salmon
</text>
<text
text-anchor=
"middle"
x=
"1139.5"
y=
"-226"
font-family=
"sans"
font-size=
"10.00"
>
kmer: 31
</text>
</g>
<!-- 30->33 -->
<g
id=
"edge60"
class=
"edge"
>
<title>
30
->
33
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1087.56,-287.7C1096,-279.14 1106.32,-268.66 1115.54,-259.3"
/>
<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
"2"
points=
"1118.11,-261.68 1122.64,-252.1 1113.13,-256.77 1118.11,-261.68"
/>
<!-- 30 -->
<g
id=
"node31"
class=
"node"
><title>
30
</title>
<path
fill=
"none"
stroke=
"#56d8a9"
stroke-width=
"2"
d=
"M1330,-617C1330,-617 1050,-617 1050,-617 1044,-617 1038,-611 1038,-605 1038,-605 1038,-593 1038,-593 1038,-587 1044,-581 1050,-581 1050,-581 1330,-581 1330,-581 1336,-581 1342,-587 1342,-593 1342,-593 1342,-605 1342,-605 1342,-611 1336,-617 1330,-617"
/>
<text
text-anchor=
"middle"
x=
"1190"
y=
"-602"
font-family=
"sans"
font-size=
"10.00"
>
remove_adapters_cutadapt
</text>
<text
text-anchor=
"middle"
x=
"1190"
y=
"-591"
font-family=
"sans"
font-size=
"10.00"
>
sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1
</text>
</g>
<!-- 31 -->
<g
id=
"node32"
class=
"node"
>
<title>
31
</title>
<path
fill=
"none"
stroke=
"#56d89a"
stroke-width=
"2"
d=
"M1423,-617C1423,-617 1110,-617 1110,-617 1104,-617 1098,-611 1098,-605 1098,-605 1098,-593 1098,-593 1098,-587 1104,-581 1110,-581 1110,-581 1423,-581 1423,-581 1429,-581 1435,-587 1435,-593 1435,-593 1435,-605 1435,-605 1435,-611 1429,-617 1423,-617"
/>
<text
text-anchor=
"middle"
x=
"1266.5"
y=
"-602"
font-family=
"sans"
font-size=
"10.00"
>
remove_adapters_cutadapt
</text>
<text
text-anchor=
"middle"
x=
"1266.5"
y=
"-591"
font-family=
"sans"
font-size=
"10.00"
>
sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1
</text>
<!-- 30->17 -->
<g
id=
"edge40"
class=
"edge"
><title>
30
->
17
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1190,-580.819C1190,-572.422 1190,-562.116 1190,-552.686"
/>
<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
"2"
points=
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/>
</g>
<!-- 31->18 -->
<g
id=
"edge46"
class=
"edge"
>
<title>
31
->
18
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1266.5,-580.82C1266.5,-572.42 1266.5,-562.12 1266.5,-552.69"
/>
<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
"2"
points=
"1270,-552.56 1266.5,-542.56 1263,-552.56 1270,-552.56"
/>
</g>
<!-- 32 -->
<g
id=
"node33"
class=
"node"
>
<title>
32
</title>
<path
fill=
"none"
stroke=
"#566bd8"
stroke-width=
"2"
d=
"M1893,-545C1893,-545 1778,-545 1778,-545 1772,-545 1766,-539 1766,-533 1766,-533 1766,-516 1766,-516 1766,-510 1772,-504 1778,-504 1778,-504 1893,-504 1893,-504 1899,-504 1905,-510 1905,-516 1905,-516 1905,-533 1905,-533 1905,-539 1899,-545 1893,-545"
/>
<text
text-anchor=
"middle"
x=
"1835.5"
y=
"-533"
font-family=
"sans"
font-size=
"10.00"
>
create_index_star
</text>
<text
text-anchor=
"middle"
x=
"1835.5"
y=
"-522"
font-family=
"sans"
font-size=
"10.00"
>
index_size: 75
</text>
<text
text-anchor=
"middle"
x=
"1835.5"
y=
"-511"
font-family=
"sans"
font-size=
"10.00"
>
organism: homo_sapiens
</text>
</g>
<!-- 32->19 -->
<g
id=
"edge47"
class=
"edge"
>
<title>
32
->
19
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1765.88,-511.04C1692.65,-497.93 1577.92,-477.39 1503.47,-464.06"
/>
<polygon
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"grey"
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"grey"
stroke-width=
"2"
points=
"1503.69,-460.55 1493.23,-462.23 1502.46,-467.44 1503.69,-460.55"
/>
</g>
<!-- 32->22 -->
<g
id=
"edge50"
class=
"edge"
>
<title>
32
->
22
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1835.5,-503.69C1835.5,-495.91 1835.5,-486.84 1835.5,-478.45"
/>
<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
"2"
points=
"1839,-478.32 1835.5,-468.32 1832,-478.32 1839,-478.32"
/>
</g>
<!-- 32->27 -->
<g
id=
"edge58"
class=
"edge"
>
<title>
32
->
27
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1888.04,-503.93C1932.59,-484.19 1993.58,-448.99 2021.5,-396 2044.78,-351.82 2024.92,-324.18 1990.5,-288 1977.81,-274.66 1961.04,-264.22 1944.52,-256.27"
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<polygon
fill=
"grey"
stroke=
"grey"
stroke-width=
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points=
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/>
</g>
<!-- 33->24 -->
<g
id=
"edge54"
class=
"edge"
>
<title>
33
->
24
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1111.12,-215.88C1095.96,-206.72 1077.09,-195.34 1060.76,-185.48"
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<polygon
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</g>
<!-- 33->25 -->
<g
id=
"edge56"
class=
"edge"
>
<title>
33
->
25
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1148.4,-215.7C1152.5,-207.73 1157.45,-198.1 1161.99,-189.26"
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/>
<g
id=
"edge41"
class=
"edge"
><title>
31
->
18
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1498.99,-287.697C1510.81,-278.796 1525.39,-267.823 1538.18,-258.199"
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<polygon
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"grey"
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</g>
<!-- 32->18 -->
<g
id=
"edge42"
class=
"edge"
><title>
32
->
18
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M1610.4,-287.697C1603.88,-279.389 1595.93,-269.277 1588.75,-260.141"
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<polygon
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</g>
<!-- 33->19 -->
<g
id=
"edge44"
class=
"edge"
><title>
33
->
19
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M938.303,-215.697C936.187,-207.898 933.638,-198.509 931.282,-189.829"
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<polygon
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"grey"
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stroke-width=
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points=
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/>
</g>
<!-- 33->20 -->
<g
id=
"edge46"
class=
"edge"
><title>
33
->
20
</title>
<path
fill=
"none"
stroke=
"grey"
stroke-width=
"2"
d=
"M971.866,-215.876C987.295,-206.724 1006.48,-195.342 1023.1,-185.485"
/>
<polygon
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"grey"
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stroke-width=
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points=
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</g>
<!-- 34 -->
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"2"
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class=
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34
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21
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34
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extract_transcripts_as_bed12
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<g
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class=
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35
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31
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"edge"
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35
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32
</title>
<path
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56
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56
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