view test-data/test_curated_nov_anno_out.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: test-data/test_curated_nov.fasta
=== PARAMETERS USED ===
input_anno: test-data/test_curated_nov_blast_headers.tabular
input_unanno: test-data/test_curated_nov.fasta
eval_plot: test-data/test_curated_nov_eval.png
taxa_output: test-data/test_curated_nov_taxa_output.txt
circle_data: test-data/test_curated_nov_circle_data.txt
header_anno: test-data/test_curated_nov_header_anno_excel.xlsx
anno_stats: test-data/test_curated_nov_anno_out.txt
filtered_fasta: test-data/test_curated_nov_filtered.fasta
uncertain_threshold: 0.9
eval_threshold: 1e-10
use_counts: True
ignore_rank: unknown
ignore_taxonomy: environmental
bitscore_perc_cutoff: 8.0
min_bitscore: 100
ignore_obiclean_type: singleton
ignore_illuminapairend_type: pairend
min_identity: 80
min_coverage: 70
ignore_seqids: 
min_support: 1
=== END PARAMETERS ===
Filtered FASTA written to: test-data/test_curated_nov_filtered.fasta (1790 sequences)
FASTA: total headers: 2156
FASTA: headers kept after filters and min_support=1: 1790
FASTA: removed due to header filters (illumina/obiclean/etc.): 366
FASTA: removed due to low dereplicated count (<1): 0
FASTA: total invalid (header filter + low support): 366
Reading BLAST annotations: test-data/test_curated_nov_blast_headers.tabular
BLAST: total hits read: 4977
BLAST: hits kept after quality filters: 3145
BLAST: hits filtered (evalue/coverage/identity/bitscore): 1832
BLAST: hits removed due to invalid taxon: 0
BLAST: hits removed due to ignored seqids: 0
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)']
ANNOTATION: total FASTA headers considered: 1790
ANNOTATION: reads with BLAST hits: 622
ANNOTATION: reads without BLAST hits: 1168
ANNOTATION: unique annotated count (from header counts): 49571
ANNOTATION: total unique count (from FASTA): 66132
E-value plot written to: test-data/test_curated_nov_eval.png
Taxa summary written to: test-data/test_curated_nov_taxa_output.txt
Header annotations written to: test-data/test_curated_nov_header_anno_excel.xlsx
Circle diagram JSON written to: test-data/test_curated_nov_circle_data.txt
=== ANNOTATION STATISTICS ===
percentage_annotated: 28.84972170686456
annotated_sequences: 622
total_sequences: 2156
percentage_unique_annotated: 74.95766043670235
unique_annotated: 49571
total_unique: 66132