[2023-03-15 21:01:44,374] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,374] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg61fdc0a3-cca6-4ada-874e-fa40a19f2277/dqc_reference
[2023-03-15 21:01:45,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,597] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,597] [INFO] Running command: cat /var/lib/cwl/stg0023a8ea-c5df-48e3-988d-37aa41b68a39/OceanDNA-b27598.fa | prodigal -d OceanDNA-b27598/cds.fna -a OceanDNA-b27598/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:01,376] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:01,377] [INFO] Task started: HMMsearch
[2023-03-15 21:02:01,377] [INFO] Running command: hmmsearch --tblout OceanDNA-b27598/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61fdc0a3-cca6-4ada-874e-fa40a19f2277/dqc_reference/reference_markers.hmm OceanDNA-b27598/protein.faa > /dev/null
[2023-03-15 21:02:01,549] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:01,549] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0023a8ea-c5df-48e3-988d-37aa41b68a39/OceanDNA-b27598.fa]
[2023-03-15 21:02:01,570] [INFO] Query marker FASTA was written to OceanDNA-b27598/markers.fasta
[2023-03-15 21:02:01,571] [INFO] Task started: Blastn
[2023-03-15 21:02:01,571] [INFO] Running command: blastn -query OceanDNA-b27598/markers.fasta -db /var/lib/cwl/stg61fdc0a3-cca6-4ada-874e-fa40a19f2277/dqc_reference/reference_markers.fasta -out OceanDNA-b27598/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:02,143] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:02,143] [INFO] Selected 25 target genomes.
[2023-03-15 21:02:02,144] [INFO] Target genome list was writen to OceanDNA-b27598/target_genomes.txt
[2023-03-15 21:02:02,158] [INFO] Task started: fastANI
[2023-03-15 21:02:02,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg0023a8ea-c5df-48e3-988d-37aa41b68a39/OceanDNA-b27598.fa --refList OceanDNA-b27598/target_genomes.txt --output OceanDNA-b27598/fastani_result.tsv --threads 1
[2023-03-15 21:02:17,729] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:17,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61fdc0a3-cca6-4ada-874e-fa40a19f2277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:17,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61fdc0a3-cca6-4ada-874e-fa40a19f2277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:17,743] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:17,743] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:17,743] [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
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	76.7372	115	786	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	76.701	117	786	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.6599	136	786	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.5981	170	786	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.5117	112	786	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	76.4713	123	786	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	76.3947	123	786	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	76.3939	117	786	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	76.3731	115	786	95	below_threshold
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	76.2967	123	786	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	76.2602	124	786	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	76.2505	123	786	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	76.221	100	786	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	76.1832	99	786	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	76.1731	103	786	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	76.1728	66	786	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.0135	155	786	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	75.9434	106	786	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	75.9434	106	786	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.9383	97	786	95	below_threshold
Paracoccus laeviglucosivorans	strain=DSM 100094	GCA_900182695.1	1197861	1197861	type	True	75.9215	60	786	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	75.7577	87	786	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	75.7512	71	786	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	75.6505	65	786	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	75.5573	59	786	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:17,744] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27598/tc_result.tsv
[2023-03-15 21:02:17,744] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:17,744] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:17,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61fdc0a3-cca6-4ada-874e-fa40a19f2277/dqc_reference/checkm_data
[2023-03-15 21:02:17,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:17,755] [INFO] Task started: CheckM
[2023-03-15 21:02:17,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27598/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27598/checkm_input OceanDNA-b27598/checkm_result
[2023-03-15 21:02:59,966] [INFO] Task succeeded: CheckM
[2023-03-15 21:02:59,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:02:59,969] [INFO] ===== Completeness check finished =====
[2023-03-15 21:02:59,969] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:02:59,970] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27598/markers.fasta)
[2023-03-15 21:02:59,970] [INFO] Task started: Blastn
[2023-03-15 21:02:59,970] [INFO] Running command: blastn -query OceanDNA-b27598/markers.fasta -db /var/lib/cwl/stg61fdc0a3-cca6-4ada-874e-fa40a19f2277/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27598/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:00,851] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:00,852] [INFO] Selected 23 target genomes.
[2023-03-15 21:03:00,852] [INFO] Target genome list was writen to OceanDNA-b27598/target_genomes_gtdb.txt
[2023-03-15 21:03:00,995] [INFO] Task started: fastANI
[2023-03-15 21:03:00,995] [INFO] Running command: fastANI --query /var/lib/cwl/stg0023a8ea-c5df-48e3-988d-37aa41b68a39/OceanDNA-b27598.fa --refList OceanDNA-b27598/target_genomes_gtdb.txt --output OceanDNA-b27598/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:16,359] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:16,372] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:03:16,372] [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_900110775.1	s__Litorimicrobium taeanense	76.7612	124	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	76.721	116	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_003352045.1	s__JL08 sp003352045	76.7051	145	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	76.6247	114	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	76.5296	110	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.5257	162	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	76.4937	66	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	76.4353	131	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015644665.1	s__Roseobacter sp015644665	76.4303	123	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172225.1	s__Ruegeria_E litorea	76.4105	116	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643905.1	s__Marivita sp017643905	76.3772	105	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115725.1	s__Marivita cryptomonadis	76.3669	114	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	99.81	99.78	0.91	0.91	31	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	76.3626	127	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458435.1	s__Thalassobius mediterraneus	76.3084	121	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900109145.1	s__Marinovum algicola	76.3057	116	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_017743735.1	s__Shimia sp017743735	76.2735	110	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_903914075.1	s__Ruegeria sp903914075	76.2448	98	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.16	95.09	0.87	0.84	7	-
GCF_900106805.1	s__Ruegeria halocynthiae	76.205	88	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814005.1	s__Ruegeria sp000814005	76.1741	89	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	76.1731	103	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900176475.1	s__Tropicibacter naphthalenivorans	76.0598	133	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009857745.1	s__Thalassobius mangrovi	76.0236	154	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013033515.1	s__Ruegeria sp013033515	76.0028	100	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.60	97.60	0.95	0.93	6	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:16,372] [INFO] GTDB search result was written to OceanDNA-b27598/result_gtdb.tsv
[2023-03-15 21:03:16,372] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:16,375] [INFO] DFAST_QC result json was written to OceanDNA-b27598/dqc_result.json
[2023-03-15 21:03:16,375] [INFO] DFAST_QC completed!
[2023-03-15 21:03:16,375] [INFO] Total running time: 0h1m32s