annotate 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

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