annotate test-data/daan_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/daan_test_unanno.fasta
=== PARAMETERS USED ===
input_anno: test-data/daan_test.tabular
input_unanno: test-data/daan_test_unanno.fasta
eval_plot: test-data/daan_eval.png
taxa_output: test-data/daan_taxa.txt
circle_data: test-data/daan_test.txt
header_anno: test-data/daan_test.xlsx
anno_stats: test-data/daan_anno_stats.txt
filtered_fasta: test-data/daan_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: 1
=== END PARAMETERS ===
Filtered FASTA written to: test-data/daan_filtered_fasta.fasta (414 sequences)
FASTA: total headers: 532
FASTA: headers kept after filters and min_support=1: 414
FASTA: removed due to header filters (illumina/obiclean/etc.): 118
FASTA: removed due to low dereplicated count (<1): 0
FASTA: total invalid (header filter + low support): 118
Reading BLAST annotations: test-data/daan_test.tabular
BLAST: total hits read: 70
BLAST: hits kept after quality filters: 70
BLAST: hits filtered (evalue/coverage/identity/bitscore): 0
BLAST: hits removed due to invalid taxon: 0
BLAST: hits removed due to ignored seqids: 0
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)']
ANNOTATION: total FASTA headers considered: 414
ANNOTATION: reads with BLAST hits: 2
ANNOTATION: reads without BLAST hits: 412
ANNOTATION: unique annotated count (from header counts): 36
ANNOTATION: total unique count (from FASTA): 3682
E-value plot written to: test-data/daan_eval.png
Taxa summary written to: test-data/daan_taxa.txt
Header annotations written to: test-data/daan_test.xlsx
Circle diagram JSON written to: test-data/daan_test.txt
=== ANNOTATION STATISTICS ===
percentage_annotated: 0.37593984962406013
annotated_sequences: 2
total_sequences: 532
percentage_unique_annotated: 0.9777294948397609
unique_annotated: 36
total_unique: 3682