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comparison test-data/test_curated_nova_anno_out.txt @ 2:9ca209477dfd draft default tip

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planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
author onnodg
date Mon, 15 Dec 2025 16:43:36 +0000
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1:2acf82433aa4 2:9ca209477dfd
1 Starting processing for FASTA
2 === PARAMETERS USED ===
3 uncertain_threshold: 0.9
4 eval_threshold: 1e-10
5 use_counts: True
6 ignore_rank: unknown
7 ignore_taxonomy: environmental
8 bitscore_perc_cutoff: 8.0
9 min_bitscore: 100
10 ignore_obiclean_type: singleton
11 ignore_illuminapairend_type: pairend
12 min_identity: 80
13 min_coverage: 70
14 ignore_seqids:
15 min_support: 1
16 === END PARAMETERS ===
17 Filtered FASTA written succesfully(1790 sequences)
18 FASTA: total headers: 2156
19 FASTA: headers kept after filters and min_support=1: 1790
20 FASTA: removed due to header filters (illumina/obiclean/etc.): 366
21 FASTA: removed due to low dereplicated count (<1): 0
22 FASTA: total invalid (header filter + low support): 366
23 Reading BLAST annotations
24 BLAST: total hits read: 4977
25 BLAST: hits kept after quality filters: 3145
26 BLAST: hits filtered (evalue/coverage/identity/bitscore): 1832
27 BLAST: hits removed due to invalid taxon: 0
28 BLAST: hits removed due to ignored seqids: 0
29 Note: 30 BLAST q_ids not in FASTA (showing up to 10): ['M01687:460:000000000-LGY9G:1:1101:11918:3518_CONS(1)', 'M01687:460:000000000-LGY9G:1:1101:12996:3690_CONS(1)', 'M01687:460:000000000-LGY9G:1:1101:11564:11468_CONS(1)', 'M01687:460:000000000-LGY9G:1:1102:19358:5472_CONS(1)', 'M01687:460:000000000-LGY9G:1:2114:4805:4734_CONS(1)', 'M01687:460:000000000-LGY9G:1:2114:7472:19038_CONS(1)', 'M01687:460:000000000-LGY9G:1:2112:26865:11154_CONS(1)', 'M01687:460:000000000-LGY9G:1:2113:29518:11119_CONS(1)', 'M01687:460:000000000-LGY9G:1:2113:14681:23251_CONS(1)', 'M01687:460:000000000-LGY9G:1:2110:17890:1754_CONS(2)']
30 ANNOTATION: total FASTA headers considered: 1790
31 ANNOTATION: reads with BLAST hits: 622
32 ANNOTATION: reads without BLAST hits: 1168
33 ANNOTATION: unique annotated count (from header counts): 49571
34 ANNOTATION: total unique count (from FASTA): 66132
35 E-value plot written succesfully
36 Taxa summary written succesfully
37 Header annotations written succesfully
38 Circle diagram JSON written succesfully
39 === ANNOTATION STATISTICS ===
40 percentage_annotated: 28.84972170686456
41 annotated_sequences: 622
42 total_sequences: 2156
43 percentage_unique_annotated: 74.95766043670235
44 unique_annotated: 49571
45 total_unique: 66132