Mercurial > repos > onnodg > blast_annotations_processor
annotate test-data/test_curated_nova_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
| author | onnodg |
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| date | Mon, 15 Dec 2025 16:43:36 +0000 |
| parents | |
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| rev | line source |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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1 Starting processing for FASTA |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
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2 === PARAMETERS USED === |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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3 uncertain_threshold: 0.9 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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4 eval_threshold: 1e-10 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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5 use_counts: True |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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6 ignore_rank: unknown |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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7 ignore_taxonomy: environmental |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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8 bitscore_perc_cutoff: 8.0 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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9 min_bitscore: 100 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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10 ignore_obiclean_type: singleton |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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11 ignore_illuminapairend_type: pairend |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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12 min_identity: 80 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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13 min_coverage: 70 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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14 ignore_seqids: |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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15 min_support: 1 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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16 === END PARAMETERS === |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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17 Filtered FASTA written succesfully(1790 sequences) |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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18 FASTA: total headers: 2156 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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19 FASTA: headers kept after filters and min_support=1: 1790 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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20 FASTA: removed due to header filters (illumina/obiclean/etc.): 366 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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21 FASTA: removed due to low dereplicated count (<1): 0 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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22 FASTA: total invalid (header filter + low support): 366 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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23 Reading BLAST annotations |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
diff
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24 BLAST: total hits read: 4977 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
diff
changeset
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25 BLAST: hits kept after quality filters: 3145 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
diff
changeset
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26 BLAST: hits filtered (evalue/coverage/identity/bitscore): 1832 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
diff
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27 BLAST: hits removed due to invalid taxon: 0 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
diff
changeset
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28 BLAST: hits removed due to ignored seqids: 0 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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29 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)'] |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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30 ANNOTATION: total FASTA headers considered: 1790 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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31 ANNOTATION: reads with BLAST hits: 622 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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32 ANNOTATION: reads without BLAST hits: 1168 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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33 ANNOTATION: unique annotated count (from header counts): 49571 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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34 ANNOTATION: total unique count (from FASTA): 66132 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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35 E-value plot written succesfully |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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36 Taxa summary written succesfully |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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37 Header annotations written succesfully |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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38 Circle diagram JSON written succesfully |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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39 === ANNOTATION STATISTICS === |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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40 percentage_annotated: 28.84972170686456 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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41 annotated_sequences: 622 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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42 total_sequences: 2156 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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43 percentage_unique_annotated: 74.95766043670235 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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44 unique_annotated: 49571 |
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9ca209477dfd
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty
onnodg
parents:
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45 total_unique: 66132 |