[2024-01-25 18:14:05,725] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:05,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:05,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg35cb47d4-b39a-4106-a2c3-fdf64f61e712/dqc_reference
[2024-01-25 18:14:06,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:06,839] [INFO] Task started: Prodigal
[2024-01-25 18:14:06,839] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc6d6842-4780-496c-8e97-b7ec6f674577/GCF_003865405.1_ASM386540v1_genomic.fna.gz | prodigal -d GCF_003865405.1_ASM386540v1_genomic.fna/cds.fna -a GCF_003865405.1_ASM386540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:15,947] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:15,947] [INFO] Task started: HMMsearch
[2024-01-25 18:14:15,948] [INFO] Running command: hmmsearch --tblout GCF_003865405.1_ASM386540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35cb47d4-b39a-4106-a2c3-fdf64f61e712/dqc_reference/reference_markers.hmm GCF_003865405.1_ASM386540v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:16,152] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:16,153] [INFO] Found 6/6 markers.
[2024-01-25 18:14:16,186] [INFO] Query marker FASTA was written to GCF_003865405.1_ASM386540v1_genomic.fna/markers.fasta
[2024-01-25 18:14:16,186] [INFO] Task started: Blastn
[2024-01-25 18:14:16,186] [INFO] Running command: blastn -query GCF_003865405.1_ASM386540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35cb47d4-b39a-4106-a2c3-fdf64f61e712/dqc_reference/reference_markers.fasta -out GCF_003865405.1_ASM386540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:16,833] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:16,836] [INFO] Selected 25 target genomes.
[2024-01-25 18:14:16,836] [INFO] Target genome list was writen to GCF_003865405.1_ASM386540v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:16,849] [INFO] Task started: fastANI
[2024-01-25 18:14:16,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc6d6842-4780-496c-8e97-b7ec6f674577/GCF_003865405.1_ASM386540v1_genomic.fna.gz --refList GCF_003865405.1_ASM386540v1_genomic.fna/target_genomes.txt --output GCF_003865405.1_ASM386540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:33,941] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:33,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35cb47d4-b39a-4106-a2c3-fdf64f61e712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:33,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35cb47d4-b39a-4106-a2c3-fdf64f61e712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:33,956] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:14:33,956] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:33,956] [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 tangerinum	strain=YIM 102701-2	GCA_003865405.1	2488728	2488728	type	True	100.0	1081	1094	95	conclusive
Flavobacterium viscosum	strain=YIM 102796	GCA_003858535.1	2488729	2488729	type	True	79.4034	324	1094	95	below_threshold
Flavobacterium ummariense	strain=DS-12	GCA_900115115.1	913024	913024	type	True	78.5856	280	1094	95	below_threshold
Flavobacterium baculatum	strain=SNL9	GCA_008629655.1	2608000	2608000	type	True	78.2019	276	1094	95	below_threshold
Myroides marinus	strain=DSM 23048	GCA_900109075.1	703342	703342	type	True	78.1118	152	1094	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.9407	208	1094	95	below_threshold
Myroides profundi	strain=D25	GCA_000833025.1	480520	480520	type	True	77.9392	124	1094	95	below_threshold
Myroides odoratimimus	strain=NCTC11180	GCA_900453765.1	76832	76832	type	True	77.7691	134	1094	95	below_threshold
Myroides odoratimimus	strain=CCUG39352	GCA_001485415.1	76832	76832	type	True	77.7266	134	1094	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	77.7084	222	1094	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.7044	194	1094	95	below_threshold
Myroides phaeus	strain=DSM 23313	GCA_900099675.1	702745	702745	type	True	77.6416	200	1094	95	below_threshold
Flavobacterium terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	77.6337	174	1094	95	below_threshold
Flavobacterium urocaniciphilum	strain=DSM 27078	GCA_900110615.1	1299341	1299341	type	True	77.6249	221	1094	95	below_threshold
Myroides injenensis	strain=M09-0166	GCA_000246945.2	1183151	1183151	type	True	77.5247	152	1094	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.2663	138	1094	95	below_threshold
Flavobacterium aquariorum	strain=IMCC34762	GCA_003254745.1	2217670	2217670	type	True	77.2592	133	1094	95	below_threshold
Flavobacterium gelidilacus	strain=DSM 15343	GCA_000422685.1	206041	206041	type	True	77.2511	225	1094	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	77.2251	136	1094	95	below_threshold
Flavobacterium filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	77.2244	136	1094	95	below_threshold
Flavobacterium pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	77.2241	127	1094	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	77.0654	73	1094	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.471	78	1094	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.4544	99	1094	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.3918	70	1094	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:33,958] [INFO] DFAST Taxonomy check result was written to GCF_003865405.1_ASM386540v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:33,958] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:33,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:33,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35cb47d4-b39a-4106-a2c3-fdf64f61e712/dqc_reference/checkm_data
[2024-01-25 18:14:33,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:33,997] [INFO] Task started: CheckM
[2024-01-25 18:14:33,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003865405.1_ASM386540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003865405.1_ASM386540v1_genomic.fna/checkm_input GCF_003865405.1_ASM386540v1_genomic.fna/checkm_result
[2024-01-25 18:15:04,087] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:04,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:04,110] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:04,110] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:04,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003865405.1_ASM386540v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:04,111] [INFO] Task started: Blastn
[2024-01-25 18:15:04,111] [INFO] Running command: blastn -query GCF_003865405.1_ASM386540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35cb47d4-b39a-4106-a2c3-fdf64f61e712/dqc_reference/reference_markers_gtdb.fasta -out GCF_003865405.1_ASM386540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:05,089] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:05,092] [INFO] Selected 18 target genomes.
[2024-01-25 18:15:05,092] [INFO] Target genome list was writen to GCF_003865405.1_ASM386540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:05,110] [INFO] Task started: fastANI
[2024-01-25 18:15:05,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc6d6842-4780-496c-8e97-b7ec6f674577/GCF_003865405.1_ASM386540v1_genomic.fna.gz --refList GCF_003865405.1_ASM386540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003865405.1_ASM386540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:16,091] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:16,101] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:16,102] [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_003865405.1	s__Flavobacterium tangerinum	100.0	1083	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013389595.1	s__Flavobacterium sp013389595	85.5166	800	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013874595.1	s__Flavobacterium sp013874595	78.7964	295	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	0.97	0.97	3	-
GCF_900115115.1	s__Flavobacterium ummariense	78.5701	280	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360925.1	s__Flavobacterium sp002360925	78.3239	328	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151275.1	s__Flavobacterium sp004151275	78.2347	285	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108395.1	s__Flavobacterium marinum	78.2274	254	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629655.1	s__Flavobacterium baculatum	78.1998	275	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109075.1	s__Flavobacterium marinum_A	78.1318	150	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.56	0.90	0.90	4	-
GCF_001485415.1	s__Flavobacterium odoratimimum	77.7607	134	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.35	97.00	0.91	0.88	14	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	77.7288	194	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099675.1	s__Flavobacterium phaeum	77.6547	202	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483315.1	s__Flavobacterium sp002483315	77.5832	198	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246945.1	s__Flavobacterium injenense	77.5322	154	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001708385.1	s__Flavobacterium psychrophilum_A	77.1524	78	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013294005.1	s__Flavobacterium sp013294005	76.81	154	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.41	97.36	0.86	0.85	3	-
GCF_015277675.1	s__Flavobacterium soyangense	76.4447	116	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	76.2156	93	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:16,103] [INFO] GTDB search result was written to GCF_003865405.1_ASM386540v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:16,103] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:16,107] [INFO] DFAST_QC result json was written to GCF_003865405.1_ASM386540v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:16,107] [INFO] DFAST_QC completed!
[2024-01-25 18:15:16,107] [INFO] Total running time: 0h1m10s