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comparison test-data/test_log.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 input_anno: test-data/test_genbank_nov_blast.tabular
4 input_unanno: test-data/test_genbank_nov.fasta
5 eval_plot: None
6 taxa_output: None
7 circle_data: test-data/test_circ.txt
8 header_anno: test-data/test_ann.xlsx
9 anno_stats: test-data/test_log.txt
10 filtered_fasta: test-data/test_filt.fasta
11 uncertain_threshold: 0.8
12 eval_threshold: 1e-08
13 use_counts: False
14 ignore_rank: unknown
15 ignore_taxonomy: environmental
16 bitscore_perc_cutoff: 0.0
17 min_bitscore: 80
18 ignore_obiclean_type: singleton,variant
19 ignore_illuminapairend_type: pairend
20 min_identity: 70
21 min_coverage: 60
22 ignore_seqids: NC_051949
23 min_support: 2
24 === END PARAMETERS ===
25 Filtered FASTA written succesfully(121 sequences)
26 FASTA: total headers: 2156
27 FASTA: headers kept after filters and min_support=2: 121
28 FASTA: removed due to header filters (illumina/obiclean/etc.): 1972
29 FASTA: removed due to low dereplicated count (<2): 63
30 FASTA: total invalid (header filter + low support): 2035
31 Reading BLAST annotations
32 BLAST: total hits read: 21506
33 BLAST: hits kept after quality filters: 17082
34 BLAST: hits filtered (evalue/coverage/identity/bitscore): 4424
35 BLAST: hits removed due to invalid taxon: 1167
36 BLAST: hits removed due to ignored seqids: 7
37 Note: 765 BLAST q_ids not in FASTA (showing up to 10): ['M01687:460:000000000-LGY9G:1:1101:14873:1895_CONS(60)', 'M01687:460:000000000-LGY9G:1:1101:20539:2360_CONS(8)', 'M01687:460:000000000-LGY9G:1:1101:14017:2896_CONS(1)', 'M01687:460:000000000-LGY9G:1:1101:23634:3049_CONS(15)', 'M01687:460:000000000-LGY9G:1:1101:23011:3088_CONS(23)', 'M01687:460:000000000-LGY9G:1:1101:11918:3518_CONS(1)', 'M01687:460:000000000-LGY9G:1:1101:12996:3690_CONS(1)', 'M01687:460:000000000-LGY9G:1:1101:13855:3748_CONS(82)', 'M01687:460:000000000-LGY9G:1:1101:11459:4030_CONS(6)', 'M01687:460:000000000-LGY9G:1:1101:25927:4422_CONS(1)']
38 ANNOTATION: total FASTA headers considered: 121
39 ANNOTATION: reads with BLAST hits: 33
40 ANNOTATION: reads without BLAST hits: 88
41 ANNOTATION: unique annotated count (from header counts): 47339
42 ANNOTATION: total unique count (from FASTA): 60351
43 Header annotations written succesfully
44 Circle diagram JSON written succesfully
45 === ANNOTATION STATISTICS ===
46 percentage_annotated: 1.530612244897959
47 annotated_sequences: 33
48 total_sequences: 2156
49 percentage_unique_annotated: 78.43946247783798
50 unique_annotated: 47339
51 total_unique: 60351