diff test-data/test_log.txt @ 2:9ca209477dfd draft default tip

planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_log.txt	Mon Dec 15 16:43:36 2025 +0000
@@ -0,0 +1,51 @@
+Starting processing for FASTA
+=== PARAMETERS USED ===
+input_anno: test-data/test_genbank_nov_blast.tabular
+input_unanno: test-data/test_genbank_nov.fasta
+eval_plot: None
+taxa_output: None
+circle_data: test-data/test_circ.txt
+header_anno: test-data/test_ann.xlsx
+anno_stats: test-data/test_log.txt
+filtered_fasta: test-data/test_filt.fasta
+uncertain_threshold: 0.8
+eval_threshold: 1e-08
+use_counts: False
+ignore_rank: unknown
+ignore_taxonomy: environmental
+bitscore_perc_cutoff: 0.0
+min_bitscore: 80
+ignore_obiclean_type: singleton,variant
+ignore_illuminapairend_type: pairend
+min_identity: 70
+min_coverage: 60
+ignore_seqids: NC_051949
+min_support: 2
+=== END PARAMETERS ===
+Filtered FASTA written succesfully(121 sequences)
+FASTA: total headers: 2156
+FASTA: headers kept after filters and min_support=2: 121
+FASTA: removed due to header filters (illumina/obiclean/etc.): 1972
+FASTA: removed due to low dereplicated count (<2): 63
+FASTA: total invalid (header filter + low support): 2035
+Reading BLAST annotations
+BLAST: total hits read: 21506
+BLAST: hits kept after quality filters: 17082
+BLAST: hits filtered (evalue/coverage/identity/bitscore): 4424
+BLAST: hits removed due to invalid taxon: 1167
+BLAST: hits removed due to ignored seqids: 7
+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)']
+ANNOTATION: total FASTA headers considered: 121
+ANNOTATION: reads with BLAST hits: 33
+ANNOTATION: reads without BLAST hits: 88
+ANNOTATION: unique annotated count (from header counts): 47339
+ANNOTATION: total unique count (from FASTA): 60351
+Header annotations written succesfully
+Circle diagram JSON written succesfully
+=== ANNOTATION STATISTICS ===
+percentage_annotated: 1.530612244897959
+annotated_sequences: 33
+total_sequences: 2156
+percentage_unique_annotated: 78.43946247783798
+unique_annotated: 47339
+total_unique: 60351
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