Mercurial > repos > onnodg > blast_annotations_processor

comparison test-data/daan_anno_stats.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: test-data/daan_test_unanno.fasta
2 === PARAMETERS USED ===
3 input_anno: test-data/daan_test.tabular
4 input_unanno: test-data/daan_test_unanno.fasta
5 eval_plot: test-data/daan_eval.png
6 taxa_output: test-data/daan_taxa.txt
7 circle_data: test-data/daan_test.txt
8 header_anno: test-data/daan_test.xlsx
9 anno_stats: test-data/daan_anno_stats.txt
10 filtered_fasta: test-data/daan_filtered_fasta.fasta
11 uncertain_threshold: 90.0
12 eval_threshold: 1e-10
13 use_counts: False
14 ignore_rank: unkown
15 ignore_taxonomy: environmental
16 bitscore_perc_cutoff: 10.0
17 min_bitscore: 40
18 ignore_obiclean_type: singleton
19 ignore_illuminapairend_type: pairend
20 min_identity: 70
21 min_coverage: 70
22 ignore_seqids:
23 min_support: 1
24 === END PARAMETERS ===
25 Filtered FASTA written to: test-data/daan_filtered_fasta.fasta (414 sequences)
26 FASTA: total headers: 532
27 FASTA: headers kept after filters and min_support=1: 414
28 FASTA: removed due to header filters (illumina/obiclean/etc.): 118
29 FASTA: removed due to low dereplicated count (<1): 0
30 FASTA: total invalid (header filter + low support): 118
31 Reading BLAST annotations: test-data/daan_test.tabular
32 BLAST: total hits read: 70
33 BLAST: hits kept after quality filters: 70
34 BLAST: hits filtered (evalue/coverage/identity/bitscore): 0
35 BLAST: hits removed due to invalid taxon: 0
36 BLAST: hits removed due to ignored seqids: 0
37 Note: 15 BLAST q_ids not in FASTA (showing up to 10): ['M01687:476:000000000-LL5F5:1:1102:16245:9240_CONS(1)', 'M01687:476:000000000-LL5F5:1:2114:3313:18654_CONS(3)', 'M01687:476:000000000-LL5F5:1:2112:19173:20011_CONS(1)', 'M01687:476:000000000-LL5F5:1:2111:13710:23471_CONS(2)', 'M01687:476:000000000-LL5F5:1:2107:11226:8080_CONS(1)', 'M01687:476:000000000-LL5F5:1:2104:21459:14659_CONS(1)', 'M01687:476:000000000-LL5F5:1:2103:8294:17591_CONS(1)', 'M01687:476:000000000-LL5F5:1:2103:20035:24420_CONS(1)', 'M01687:476:000000000-LL5F5:1:2101:19159:13262_CONS(1)', 'M01687:476:000000000-LL5F5:1:1114:20282:19626_CONS(1)']
38 ANNOTATION: total FASTA headers considered: 414
39 ANNOTATION: reads with BLAST hits: 2
40 ANNOTATION: reads without BLAST hits: 412
41 ANNOTATION: unique annotated count (from header counts): 36
42 ANNOTATION: total unique count (from FASTA): 3682
43 E-value plot written to: test-data/daan_eval.png
44 Taxa summary written to: test-data/daan_taxa.txt
45 Header annotations written to: test-data/daan_test.xlsx
46 Circle diagram JSON written to: test-data/daan_test.txt
47 === ANNOTATION STATISTICS ===
48 percentage_annotated: 0.37593984962406013
49 annotated_sequences: 2
50 total_sequences: 532
51 percentage_unique_annotated: 0.9777294948397609
52 unique_annotated: 36
53 total_unique: 3682