[2024-01-24 11:26:37,620] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:37,623] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:37,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg114ea16a-71be-443a-ad38-74974861cdea/dqc_reference
[2024-01-24 11:26:38,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:38,957] [INFO] Task started: Prodigal
[2024-01-24 11:26:38,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c85bbe4-6faf-459f-a3f2-f1994f24dfa1/GCF_003944795.1_FEB-2018_genomic.fna.gz | prodigal -d GCF_003944795.1_FEB-2018_genomic.fna/cds.fna -a GCF_003944795.1_FEB-2018_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:47,722] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:47,722] [INFO] Task started: HMMsearch
[2024-01-24 11:26:47,722] [INFO] Running command: hmmsearch --tblout GCF_003944795.1_FEB-2018_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg114ea16a-71be-443a-ad38-74974861cdea/dqc_reference/reference_markers.hmm GCF_003944795.1_FEB-2018_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:47,991] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:47,992] [INFO] Found 6/6 markers.
[2024-01-24 11:26:48,016] [INFO] Query marker FASTA was written to GCF_003944795.1_FEB-2018_genomic.fna/markers.fasta
[2024-01-24 11:26:48,016] [INFO] Task started: Blastn
[2024-01-24 11:26:48,017] [INFO] Running command: blastn -query GCF_003944795.1_FEB-2018_genomic.fna/markers.fasta -db /var/lib/cwl/stg114ea16a-71be-443a-ad38-74974861cdea/dqc_reference/reference_markers.fasta -out GCF_003944795.1_FEB-2018_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:48,687] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:48,690] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:48,690] [INFO] Target genome list was writen to GCF_003944795.1_FEB-2018_genomic.fna/target_genomes.txt
[2024-01-24 11:26:48,716] [INFO] Task started: fastANI
[2024-01-24 11:26:48,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c85bbe4-6faf-459f-a3f2-f1994f24dfa1/GCF_003944795.1_FEB-2018_genomic.fna.gz --refList GCF_003944795.1_FEB-2018_genomic.fna/target_genomes.txt --output GCF_003944795.1_FEB-2018_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:59,518] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:59,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg114ea16a-71be-443a-ad38-74974861cdea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:59,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg114ea16a-71be-443a-ad38-74974861cdea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:59,542] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:59,542] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:59,543] [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
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	100.0	919	920	95	conclusive
Mangrovimonas yunxiaonensis	strain=LY01	GCA_000733475.1	1197477	1197477	type	True	80.5884	495	920	95	below_threshold
Mangrovimonas yunxiaonensis	strain=CGMCC 1.12280	GCA_014636995.1	1197477	1197477	type	True	80.5332	496	920	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.932	276	920	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.7773	285	920	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.7678	245	920	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	77.7199	265	920	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	77.6989	257	920	95	below_threshold
Tamlana sedimentorum	strain=JCM 19808	GCA_000943565.1	1435349	1435349	type	True	77.6888	249	920	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.5346	251	920	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	77.4931	261	920	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.4715	188	920	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.4043	230	920	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.2284	181	920	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	77.199	191	920	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.1541	221	920	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.067	223	920	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.0288	210	920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:59,544] [INFO] DFAST Taxonomy check result was written to GCF_003944795.1_FEB-2018_genomic.fna/tc_result.tsv
[2024-01-24 11:26:59,545] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:59,545] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:59,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg114ea16a-71be-443a-ad38-74974861cdea/dqc_reference/checkm_data
[2024-01-24 11:26:59,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:59,579] [INFO] Task started: CheckM
[2024-01-24 11:26:59,580] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003944795.1_FEB-2018_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003944795.1_FEB-2018_genomic.fna/checkm_input GCF_003944795.1_FEB-2018_genomic.fna/checkm_result
[2024-01-24 11:27:29,620] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:29,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:29,642] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:29,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:29,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003944795.1_FEB-2018_genomic.fna/markers.fasta)
[2024-01-24 11:27:29,644] [INFO] Task started: Blastn
[2024-01-24 11:27:29,644] [INFO] Running command: blastn -query GCF_003944795.1_FEB-2018_genomic.fna/markers.fasta -db /var/lib/cwl/stg114ea16a-71be-443a-ad38-74974861cdea/dqc_reference/reference_markers_gtdb.fasta -out GCF_003944795.1_FEB-2018_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:30,546] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:30,550] [INFO] Selected 21 target genomes.
[2024-01-24 11:27:30,550] [INFO] Target genome list was writen to GCF_003944795.1_FEB-2018_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:30,573] [INFO] Task started: fastANI
[2024-01-24 11:27:30,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c85bbe4-6faf-459f-a3f2-f1994f24dfa1/GCF_003944795.1_FEB-2018_genomic.fna.gz --refList GCF_003944795.1_FEB-2018_genomic.fna/target_genomes_gtdb.txt --output GCF_003944795.1_FEB-2018_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:42,991] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:43,012] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:43,012] [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_003944795.1	s__Mangrovimonas spongiae	100.0	919	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000733475.1	s__Mangrovimonas yunxiaonensis	80.5763	496	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	98.99	97.98	0.98	0.97	3	-
GCF_004366715.1	s__Meridianimaribacter flavus	78.4235	340	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCA_002722255.1	s__Winogradskyella sp002722255	78.1084	216	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	77.9289	291	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_008084905.1	s__Xanthomarina maritima	77.8928	303	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115185.1	s__Algorimicrobium echini	77.7314	264	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	97.77	97.77	0.81	0.81	2	-
GCF_012931685.1	s__Pseudobizionia ponticola	77.6989	257	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
GCA_003144015.1	s__Xanthomarina sp003144015	77.6618	295	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869935.1	s__Winogradskyella algicola	77.6388	213	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	77.5694	310	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.5495	246	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	77.5346	251	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	77.5162	259	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002366675.1	s__Xanthomarina sp002366675	77.509	236	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	77.4882	187	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	77.4441	216	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	77.3691	295	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163855.1	s__Winogradskyella sp002163855	77.2306	180	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCF_004310335.1	s__Jejuia pacifica	77.199	191	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003337305.1	s__Winogradskyella arenosi	77.0631	196	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:43,014] [INFO] GTDB search result was written to GCF_003944795.1_FEB-2018_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:43,015] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:43,019] [INFO] DFAST_QC result json was written to GCF_003944795.1_FEB-2018_genomic.fna/dqc_result.json
[2024-01-24 11:27:43,019] [INFO] DFAST_QC completed!
[2024-01-24 11:27:43,019] [INFO] Total running time: 0h1m5s