[2023-03-18 08:17:18,487] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:18,487] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:18,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d9ae744-4128-4c7c-9856-d54777aa3229/dqc_reference
[2023-03-18 08:17:20,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:20,265] [INFO] Task started: Prodigal
[2023-03-18 08:17:20,265] [INFO] Running command: cat /var/lib/cwl/stgbebe6984-50d7-40b5-a8c3-fce3f4f28565/OceanDNA-b27600.fa | prodigal -d OceanDNA-b27600/cds.fna -a OceanDNA-b27600/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:36,131] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:36,132] [INFO] Task started: HMMsearch
[2023-03-18 08:17:36,132] [INFO] Running command: hmmsearch --tblout OceanDNA-b27600/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d9ae744-4128-4c7c-9856-d54777aa3229/dqc_reference/reference_markers.hmm OceanDNA-b27600/protein.faa > /dev/null
[2023-03-18 08:17:36,310] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:36,310] [INFO] Found 6/6 markers.
[2023-03-18 08:17:36,330] [INFO] Query marker FASTA was written to OceanDNA-b27600/markers.fasta
[2023-03-18 08:17:36,330] [INFO] Task started: Blastn
[2023-03-18 08:17:36,330] [INFO] Running command: blastn -query OceanDNA-b27600/markers.fasta -db /var/lib/cwl/stg0d9ae744-4128-4c7c-9856-d54777aa3229/dqc_reference/reference_markers.fasta -out OceanDNA-b27600/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:37,002] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:37,003] [INFO] Selected 37 target genomes.
[2023-03-18 08:17:37,003] [INFO] Target genome list was writen to OceanDNA-b27600/target_genomes.txt
[2023-03-18 08:17:37,019] [INFO] Task started: fastANI
[2023-03-18 08:17:37,019] [INFO] Running command: fastANI --query /var/lib/cwl/stgbebe6984-50d7-40b5-a8c3-fce3f4f28565/OceanDNA-b27600.fa --refList OceanDNA-b27600/target_genomes.txt --output OceanDNA-b27600/fastani_result.tsv --threads 1
[2023-03-18 08:18:01,855] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:01,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d9ae744-4128-4c7c-9856-d54777aa3229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:18:01,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d9ae744-4128-4c7c-9856-d54777aa3229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:18:01,873] [INFO] Found 35 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:18:01,873] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:18:01,873] [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
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	77.5943	144	846	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	77.4999	148	846	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	77.3204	159	846	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.1697	175	846	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.1505	176	846	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	77.1068	165	846	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.0044	166	846	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.9364	158	846	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	76.9077	146	846	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	76.9073	145	846	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	76.9	184	846	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	76.8701	153	846	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.8607	105	846	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.8241	125	846	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.7115	142	846	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	76.7058	129	846	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.6959	116	846	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	76.6904	93	846	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	76.6841	113	846	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.6611	89	846	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	76.628	116	846	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.6246	102	846	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	76.6229	112	846	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	76.6201	144	846	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	76.6084	109	846	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	76.5819	89	846	95	below_threshold
Paracoccus sulfuroxidans	strain=CGMCC 1.5364	GCA_007830335.1	384678	384678	type	True	76.475	82	846	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	76.4619	93	846	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.3607	83	846	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.3119	101	846	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	76.2123	105	846	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.1117	71	846	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	75.9504	77	846	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	75.7676	118	846	95	below_threshold
Tropicimonas isoalkanivorans	strain=DSM 19548	GCA_900112335.1	441112	441112	type	True	75.5185	57	846	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:18:01,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27600/tc_result.tsv
[2023-03-18 08:18:01,873] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:18:01,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:18:01,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d9ae744-4128-4c7c-9856-d54777aa3229/dqc_reference/checkm_data
[2023-03-18 08:18:01,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:18:01,879] [INFO] Task started: CheckM
[2023-03-18 08:18:01,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27600/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27600/checkm_input OceanDNA-b27600/checkm_result
[2023-03-18 08:18:43,976] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:43,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:43,979] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:43,979] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:43,979] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27600/markers.fasta)
[2023-03-18 08:18:43,980] [INFO] Task started: Blastn
[2023-03-18 08:18:43,980] [INFO] Running command: blastn -query OceanDNA-b27600/markers.fasta -db /var/lib/cwl/stg0d9ae744-4128-4c7c-9856-d54777aa3229/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27600/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:45,090] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:45,091] [INFO] Selected 38 target genomes.
[2023-03-18 08:18:45,091] [INFO] Target genome list was writen to OceanDNA-b27600/target_genomes_gtdb.txt
[2023-03-18 08:18:45,203] [INFO] Task started: fastANI
[2023-03-18 08:18:45,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgbebe6984-50d7-40b5-a8c3-fce3f4f28565/OceanDNA-b27600.fa --refList OceanDNA-b27600/target_genomes_gtdb.txt --output OceanDNA-b27600/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:19:09,564] [INFO] Task succeeded: fastANI
[2023-03-18 08:19:09,584] [INFO] Found 38 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:19:09,584] [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_002285415.1	s__Actibacterium pelagium	77.4963	146	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001458255.1	s__Thalassobius autumnalis	77.3204	159	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_900114635.1	s__Shimia aestuarii	77.2724	160	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	77.2146	176	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744095.1	s__Shimia sp017744095	77.1722	110	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.161	174	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	77.1505	176	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	77.0971	164	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	77.0905	149	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031355.1	s__Ruegeria arenilitoris_C	77.0479	166	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.51	99.51	0.98	0.98	2	-
GCF_003443535.1	s__Ruegeria sp003443535	77.0344	128	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	77.0243	167	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	76.9559	147	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014872875.1	s__WKFI01 sp014872875	76.9056	134	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__WKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	76.8928	149	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_000511355.1	s__Leisingera methylohalidivorans	76.8656	151	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813725.1	s__Leisingera sp000813725	76.7873	178	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	76.6817	142	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115165.1	s__Roseovarius lutimaris	76.6786	115	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176475.1	s__Tropicibacter naphthalenivorans	76.6672	137	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000152805.1	s__Maritimibacter alkaliphilus	76.6662	112	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	97.94	96.90	0.93	0.88	4	-
GCF_001458335.1	s__Cognatishimia activa	76.6637	93	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	99.97	99.97	0.99	0.99	2	-
GCF_900156505.1	s__Yoonia rosea	76.6018	87	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	76.5908	158	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900172335.1	s__Roseovarius albus	76.584	100	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830335.1	s__Paracoccus sulfuroxidans	76.5002	81	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419985.1	s__Yoonia sp001419985	76.4874	94	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.4805	127	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458355.1	s__Thalassobius gelatinovorus	76.4754	128	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	99.99	0.99	0.99	3	-
GCF_900156535.1	s__Roseovarius nanhaiticus	76.4564	86	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003316635.1	s__Roseovarius dicentrarchi	76.4376	92	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	76.4033	114	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378665.1	s__Yoonia sp002378665	76.3242	70	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	99.59	99.15	0.91	0.87	4	-
GCA_002842985.1	s__Roseovarius sp002842985	76.2932	82	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	76.2922	99	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	76.2219	103	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	76.1906	119	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113875.1	s__Jannaschia pohangensis	75.9144	76	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:19:09,584] [INFO] GTDB search result was written to OceanDNA-b27600/result_gtdb.tsv
[2023-03-18 08:19:09,584] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:19:09,588] [INFO] DFAST_QC result json was written to OceanDNA-b27600/dqc_result.json
[2023-03-18 08:19:09,588] [INFO] DFAST_QC completed!
[2023-03-18 08:19:09,588] [INFO] Total running time: 0h1m51s