annotate test-data/consensus_anno_stats.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/consensus_anno_test.fasta
=== PARAMETERS USED ===
input_anno: test-data/consensus_test_header.tabular
input_unanno: test-data/consensus_anno_test.fasta
eval_plot: test-data/consensus_eval.png
taxa_output: test-data/consensus_taxa.txt
circle_data: test-data/consensus_circle.txt
header_anno: test-data/consensus_annotations.xlsx
anno_stats: test-data/consensus_anno_stats.txt
filtered_fasta: test-data/consensus_filtered_fasta.fasta
uncertain_threshold: 90.0
eval_threshold: 1e-10
use_counts: False
ignore_rank: unkown
ignore_taxonomy: environmental
bitscore_perc_cutoff: 10.0
min_bitscore: 40
ignore_obiclean_type: singleton
ignore_illuminapairend_type: pairend
min_identity: 70
min_coverage: 70
ignore_seqids: 
min_support: 2
=== END PARAMETERS ===
Filtered FASTA written to: test-data/consensus_filtered_fasta.fasta (269 sequences)
FASTA: total headers: 1937
FASTA: headers kept after filters and min_support=2: 269
FASTA: removed due to header filters (illumina/obiclean/etc.): 365
FASTA: removed due to low dereplicated count (<2): 1303
FASTA: total invalid (header filter + low support): 1668
Reading BLAST annotations: test-data/consensus_test_header.tabular
BLAST: total hits read: 889
BLAST: hits kept after quality filters: 767
BLAST: hits filtered (evalue/coverage/identity/bitscore): 122
BLAST: hits removed due to invalid taxon: 0
BLAST: hits removed due to ignored seqids: 0
Note: 37 BLAST q_ids not in FASTA (showing up to 10): ['M01687:460:000000000-LGY9G:1:1101:12578:8821_CONS(1)', 'M01687:460:000000000-LGY9G:1:1102:19139:9563_CONS(1)', 'M01687:460:000000000-LGY9G:1:2114:3286:13205_CONS(1)', 'M01687:460:000000000-LGY9G:1:2115:26033:6510_CONS(1)', 'M01687:460:000000000-LGY9G:1:2115:28971:12582_CONS(1)', 'M01687:460:000000000-LGY9G:1:2115:9332:15134_CONS(1)', 'M01687:460:000000000-LGY9G:1:2112:16849:24934_CONS(1)', 'M01687:460:000000000-LGY9G:1:2113:2910:9568_CONS(2)', 'M01687:460:000000000-LGY9G:1:2113:24519:22653_CONS(1)', 'M01687:460:000000000-LGY9G:1:2108:19954:3938_CONS(1)']
ANNOTATION: total FASTA headers considered: 269
ANNOTATION: reads with BLAST hits: 4
ANNOTATION: reads without BLAST hits: 265
ANNOTATION: unique annotated count (from header counts): 384
ANNOTATION: total unique count (from FASTA): 24251
E-value plot written to: test-data/consensus_eval.png
Taxa summary written to: test-data/consensus_taxa.txt
Header annotations written to: test-data/consensus_annotations.xlsx
Circle diagram JSON written to: test-data/consensus_circle.txt
=== ANNOTATION STATISTICS ===
percentage_annotated: 0.20650490449148168
annotated_sequences: 4
total_sequences: 1937
percentage_unique_annotated: 1.5834398581501794
unique_annotated: 384
total_unique: 24251