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annotate test-data/groot.log @ 0:fbe36cf83eb7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
author iuc
date Fri, 18 Oct 2024 08:19:14 +0000
parents
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
1 2024/10/15 11:32:06 i am groot (version 1.1.2)
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
2 2024/10/15 11:32:06 starting the index subcommand
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
3 2024/10/15 11:32:06 checking parameters...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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4 2024/10/15 11:32:06 directory containing MSA files: arg-annot.90
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
5 2024/10/15 11:32:06 number of MSA files: 12
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
6 2024/10/15 11:32:06 processors: 1
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
7 2024/10/15 11:32:06 k-mer size: 41
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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8 2024/10/15 11:32:06 sketch size: 21
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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9 2024/10/15 11:32:06 graph window size: 150
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
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10 2024/10/15 11:32:06 num. partitions: 8
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
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11 2024/10/15 11:32:06 max. K: 4
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
12 2024/10/15 11:32:06 max. sketch span: 30
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
13 2024/10/15 11:32:06 initialising indexing pipeline...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
14 2024/10/15 11:32:06 initialising the processes
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
15 2024/10/15 11:32:06 connecting data streams
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
16 2024/10/15 11:32:06 number of processes added to the indexing pipeline: 3
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
17 2024/10/15 11:32:06 creating graphs, sketching traversals and indexing...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
18 2024/10/15 11:32:07 number of groot graphs built: 12
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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19 2024/10/15 11:32:07 graphs sketched: 12
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
20 2024/10/15 11:32:07 graph windows processed: 35387
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
21 2024/10/15 11:32:07 mean approximate distinct sketches per graph: 29.20%
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
22 2024/10/15 11:32:07 number of sketches added to the LSH Ensemble index: 5155
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
23 2024/10/15 11:32:07 writing index files in "grootIndex"...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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24 2024/10/15 11:32:07 finished in 685.70958ms
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
25 2024/10/15 11:32:39 i am groot (version 1.1.2)
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
26 2024/10/15 11:32:39 starting the sketch subcommand
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
27 2024/10/15 11:32:39 checking parameters...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
28 2024/10/15 11:32:39 terminated
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
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29
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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30 ERROR --> file does not exist: argannot-150bp-10000-reads.fq.gz
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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31
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
32 2024/10/15 11:33:04 i am groot (version 1.1.2)
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
33 2024/10/15 11:33:04 starting the sketch subcommand
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
34 2024/10/15 11:33:04 checking parameters...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
35 2024/10/15 11:33:04 minimum k-mer coverage: 1
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
36 2024/10/15 11:33:04 processors: 1
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
37 2024/10/15 11:33:04 input file: argannot_light-150bp-10000-reads.fq.gz
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
38 2024/10/15 11:33:04 loading the index information...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
39 2024/10/15 11:33:04 k-mer size: 41
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
40 2024/10/15 11:33:04 sketch size: 21
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
41 2024/10/15 11:33:04 window size used in indexing: 150
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
42 2024/10/15 11:33:04 loading the graphs...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
43 2024/10/15 11:33:04 number of variation graphs: 12
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
44 2024/10/15 11:33:04 rebuilding the LSH Ensemble...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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45 2024/10/15 11:33:04 containment threshold: 0.99
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
46 2024/10/15 11:33:04 initialising alignment pipeline...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
47 2024/10/15 11:33:04 initialising the processes
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
48 2024/10/15 11:33:04 connecting data streams
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
49 2024/10/15 11:33:04 number of processes added to the alignment pipeline: 5
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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50 2024/10/15 11:33:04 now streaming reads...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
51 2024/10/15 11:33:04 number of reads received from input: 5000
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
52 2024/10/15 11:33:04 mean read length: 150
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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53 2024/10/15 11:33:04 number of reads sketched: 5000
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
54 2024/10/15 11:33:04 total number of unmapped reads: 4873
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
55 2024/10/15 11:33:04 total number of mapped reads: 127
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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56 2024/10/15 11:33:04 mapped to one graph: 127
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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57 2024/10/15 11:33:04 mapped to multiple graphs: 0
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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58 2024/10/15 11:33:04 total number of exact alignments: 954
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
59 2024/10/15 11:33:04 processing graphs...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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60 2024/10/15 11:33:04 total number of k-mers projected onto graphs: 10890
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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61 2024/10/15 11:33:04 graph 7 has 4 remaining paths after weighting and pruning
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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62 2024/10/15 11:33:04 - [*argannot~~~(Bla)cfxA2~~~AF504910:1-966]
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
63 2024/10/15 11:33:04 - [argannot~~~(Bla)cfxA4~~~AY769933:1-966]
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
64 2024/10/15 11:33:04 - [argannot~~~(Bla)cfxA5~~~AY769934:28-993]
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
65 2024/10/15 11:33:04 - [argannot~~~(Bla)cfxA~~~U38243:150-1115]
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
66 2024/10/15 11:33:04 total number of graphs pruned: 12
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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67 2024/10/15 11:33:04 total number of graphs remaining: 1
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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68 2024/10/15 11:33:04 total number of possible haplotypes found: 4
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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69 2024/10/15 11:33:04 saving graphs...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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70 2024/10/15 11:33:04 finished in 223.277576ms
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
71 2024/10/15 11:33:15 i am groot (version 1.1.2)
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
72 2024/10/15 11:33:15 starting the report subcommand
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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73 2024/10/15 11:33:15 checking parameters...
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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74 2024/10/15 11:33:15 BAM file: groot.bam
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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75 2024/10/15 11:33:15 coverage cutoff: 0.97
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
diff changeset
76 2024/10/15 11:33:15 processors: 1
fbe36cf83eb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
parents:
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77 2024/10/15 11:33:15 finished