[2024-01-24 12:44:43,378] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,380] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,381] [INFO] DQC Reference Directory: /var/lib/cwl/stg520bfb5b-4830-42d1-89ca-25b0eaddd489/dqc_reference
[2024-01-24 12:44:44,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:44,837] [INFO] Task started: Prodigal
[2024-01-24 12:44:44,838] [INFO] Running command: gunzip -c /var/lib/cwl/stga82514e3-ae6d-43da-ba28-2730da234cf6/GCF_014305155.1_ASM1430515v1_genomic.fna.gz | prodigal -d GCF_014305155.1_ASM1430515v1_genomic.fna/cds.fna -a GCF_014305155.1_ASM1430515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:00,167] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:00,167] [INFO] Task started: HMMsearch
[2024-01-24 12:45:00,167] [INFO] Running command: hmmsearch --tblout GCF_014305155.1_ASM1430515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg520bfb5b-4830-42d1-89ca-25b0eaddd489/dqc_reference/reference_markers.hmm GCF_014305155.1_ASM1430515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:00,511] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:00,512] [INFO] Found 6/6 markers.
[2024-01-24 12:45:00,549] [INFO] Query marker FASTA was written to GCF_014305155.1_ASM1430515v1_genomic.fna/markers.fasta
[2024-01-24 12:45:00,550] [INFO] Task started: Blastn
[2024-01-24 12:45:00,550] [INFO] Running command: blastn -query GCF_014305155.1_ASM1430515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg520bfb5b-4830-42d1-89ca-25b0eaddd489/dqc_reference/reference_markers.fasta -out GCF_014305155.1_ASM1430515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:01,229] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:01,232] [INFO] Selected 20 target genomes.
[2024-01-24 12:45:01,232] [INFO] Target genome list was writen to GCF_014305155.1_ASM1430515v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:01,242] [INFO] Task started: fastANI
[2024-01-24 12:45:01,242] [INFO] Running command: fastANI --query /var/lib/cwl/stga82514e3-ae6d-43da-ba28-2730da234cf6/GCF_014305155.1_ASM1430515v1_genomic.fna.gz --refList GCF_014305155.1_ASM1430515v1_genomic.fna/target_genomes.txt --output GCF_014305155.1_ASM1430515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:16,332] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:16,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg520bfb5b-4830-42d1-89ca-25b0eaddd489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:16,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg520bfb5b-4830-42d1-89ca-25b0eaddd489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:16,348] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:16,349] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:16,349] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	100.0	1321	1324	95	conclusive
Flavobacterium frigidarium	strain=DSM 17623	GCA_000425505.1	99286	99286	type	True	82.2563	578	1324	95	below_threshold
Flavobacterium kayseriense	strain=F-47	GCA_014305095.1	2764714	2764714	type	True	80.9293	523	1324	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	80.2552	610	1324	95	below_threshold
Flavobacterium gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	80.2136	618	1324	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	79.9718	523	1324	95	below_threshold
Flavobacterium crassostreae	strain=LPB0076	GCA_001831475.1	1763534	1763534	type	True	79.9598	417	1324	95	below_threshold
Flavobacterium faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	79.6857	413	1324	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	79.4263	452	1324	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.3136	497	1324	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	79.2192	413	1324	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	79.1355	472	1324	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	79.1148	440	1324	95	below_threshold
Flavobacterium omnivorum	strain=CGMCC 1.2747	GCA_900099915.1	178355	178355	type	True	79.058	437	1324	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	78.9887	429	1324	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.5676	424	1324	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	77.8285	256	1324	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.5699	161	1324	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.3896	191	1324	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:16,355] [INFO] DFAST Taxonomy check result was written to GCF_014305155.1_ASM1430515v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:16,356] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:16,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:16,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg520bfb5b-4830-42d1-89ca-25b0eaddd489/dqc_reference/checkm_data
[2024-01-24 12:45:16,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:16,402] [INFO] Task started: CheckM
[2024-01-24 12:45:16,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014305155.1_ASM1430515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014305155.1_ASM1430515v1_genomic.fna/checkm_input GCF_014305155.1_ASM1430515v1_genomic.fna/checkm_result
[2024-01-24 12:46:02,212] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:02,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:02,241] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:02,242] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:02,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014305155.1_ASM1430515v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:02,243] [INFO] Task started: Blastn
[2024-01-24 12:46:02,243] [INFO] Running command: blastn -query GCF_014305155.1_ASM1430515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg520bfb5b-4830-42d1-89ca-25b0eaddd489/dqc_reference/reference_markers_gtdb.fasta -out GCF_014305155.1_ASM1430515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:03,163] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:03,167] [INFO] Selected 13 target genomes.
[2024-01-24 12:46:03,167] [INFO] Target genome list was writen to GCF_014305155.1_ASM1430515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:03,181] [INFO] Task started: fastANI
[2024-01-24 12:46:03,181] [INFO] Running command: fastANI --query /var/lib/cwl/stga82514e3-ae6d-43da-ba28-2730da234cf6/GCF_014305155.1_ASM1430515v1_genomic.fna.gz --refList GCF_014305155.1_ASM1430515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014305155.1_ASM1430515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:12,956] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:12,972] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:12,972] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014305155.1	s__Flavobacterium sp014305155	100.0	1321	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000425505.1	s__Flavobacterium frigidarium	82.2728	577	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294005.1	s__Flavobacterium sp013294005	81.4331	664	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.41	97.36	0.86	0.85	3	-
GCF_013294025.1	s__Flavobacterium sp013294025	81.0808	558	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014305095.1	s__Flavobacterium kayseriense	80.9337	523	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.16	98.32	0.96	0.92	3	-
GCF_000252125.1	s__Flavobacterium frigoris_A	80.2901	578	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106645.1	s__Flavobacterium degerlachei	80.2675	609	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107635.1	s__Flavobacterium gillisiae	80.2242	616	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111075.1	s__Flavobacterium frigoris	79.9139	566	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754315.1	s__Flavobacterium sp002754315	79.5523	483	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_002836475.1	s__Flavobacterium sp002836475	79.2609	471	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108015.1	s__Flavobacterium urumqiense	79.0961	476	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099915.1	s__Flavobacterium omnivorum	79.0368	439	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:12,977] [INFO] GTDB search result was written to GCF_014305155.1_ASM1430515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:12,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:12,986] [INFO] DFAST_QC result json was written to GCF_014305155.1_ASM1430515v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:12,986] [INFO] DFAST_QC completed!
[2024-01-24 12:46:12,986] [INFO] Total running time: 0h1m30s