[2023-03-15 09:48:18,595] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:18,595] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:18,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg32e5d660-7b7c-4c49-8c6e-f121242641ee/dqc_reference
[2023-03-15 09:48:19,794] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:19,794] [INFO] Task started: Prodigal
[2023-03-15 09:48:19,795] [INFO] Running command: cat /var/lib/cwl/stgb06c5b46-f386-447d-8198-5c2cf08ca0cd/OceanDNA-b39168.fa | prodigal -d OceanDNA-b39168/cds.fna -a OceanDNA-b39168/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:44,350] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:44,351] [INFO] Task started: HMMsearch
[2023-03-15 09:48:44,351] [INFO] Running command: hmmsearch --tblout OceanDNA-b39168/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32e5d660-7b7c-4c49-8c6e-f121242641ee/dqc_reference/reference_markers.hmm OceanDNA-b39168/protein.faa > /dev/null
[2023-03-15 09:48:44,614] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:44,614] [INFO] Found 6/6 markers.
[2023-03-15 09:48:44,636] [INFO] Query marker FASTA was written to OceanDNA-b39168/markers.fasta
[2023-03-15 09:48:44,636] [INFO] Task started: Blastn
[2023-03-15 09:48:44,636] [INFO] Running command: blastn -query OceanDNA-b39168/markers.fasta -db /var/lib/cwl/stg32e5d660-7b7c-4c49-8c6e-f121242641ee/dqc_reference/reference_markers.fasta -out OceanDNA-b39168/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:45,353] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:45,354] [INFO] Selected 28 target genomes.
[2023-03-15 09:48:45,354] [INFO] Target genome list was writen to OceanDNA-b39168/target_genomes.txt
[2023-03-15 09:48:45,370] [INFO] Task started: fastANI
[2023-03-15 09:48:45,370] [INFO] Running command: fastANI --query /var/lib/cwl/stgb06c5b46-f386-447d-8198-5c2cf08ca0cd/OceanDNA-b39168.fa --refList OceanDNA-b39168/target_genomes.txt --output OceanDNA-b39168/fastani_result.tsv --threads 1
[2023-03-15 09:49:05,073] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:05,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32e5d660-7b7c-4c49-8c6e-f121242641ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:49:05,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32e5d660-7b7c-4c49-8c6e-f121242641ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:49:05,086] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:49:05,086] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:49:05,086] [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
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	78.1765	450	1313	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	78.1211	418	1313	95	below_threshold
Marinobacter fonticola	strain=CS412	GCA_008122265.1	2603215	2603215	type	True	78.0969	393	1313	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	78.0481	433	1313	95	below_threshold
Marinobacter nanhaiticus	strain=D15-8W	GCA_000364845.1	1305740	1305740	type	True	78.0242	381	1313	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	77.883	193	1313	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	77.8587	247	1313	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	77.8345	222	1313	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.7535	246	1313	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	77.6376	235	1313	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	77.6184	212	1313	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_007559285.1	1928331	1928331	type	True	77.6153	212	1313	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_003344045.1	1928331	1928331	type	True	77.5752	212	1313	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	77.5645	246	1313	95	below_threshold
Marinobacter litoralis	strain=Sw-45	GCA_003336705.1	187981	187981	type	True	77.4549	191	1313	95	below_threshold
Marinobacter changyiensis	strain=CLL7-20	GCA_009193265.1	2604091	2604091	type	True	77.4538	223	1313	95	below_threshold
Marinobacter halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	77.3908	223	1313	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	77.3799	240	1313	95	below_threshold
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	77.3094	243	1313	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	77.2706	273	1313	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	77.2616	234	1313	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	77.2275	203	1313	95	below_threshold
Pseudomonas pohangensis	strain=DSM 17875	GCA_900105995.1	364197	364197	type	True	75.9273	57	1313	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	75.81	50	1313	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:49:05,086] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39168/tc_result.tsv
[2023-03-15 09:49:05,086] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:49:05,086] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:49:05,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32e5d660-7b7c-4c49-8c6e-f121242641ee/dqc_reference/checkm_data
[2023-03-15 09:49:05,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:49:05,097] [INFO] Task started: CheckM
[2023-03-15 09:49:05,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39168/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39168/checkm_input OceanDNA-b39168/checkm_result
[2023-03-15 09:50:06,544] [INFO] Task succeeded: CheckM
[2023-03-15 09:50:06,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:50:06,547] [INFO] ===== Completeness check finished =====
[2023-03-15 09:50:06,547] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:50:06,547] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39168/markers.fasta)
[2023-03-15 09:50:06,547] [INFO] Task started: Blastn
[2023-03-15 09:50:06,547] [INFO] Running command: blastn -query OceanDNA-b39168/markers.fasta -db /var/lib/cwl/stg32e5d660-7b7c-4c49-8c6e-f121242641ee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39168/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:50:07,710] [INFO] Task succeeded: Blastn
[2023-03-15 09:50:07,711] [INFO] Selected 20 target genomes.
[2023-03-15 09:50:07,711] [INFO] Target genome list was writen to OceanDNA-b39168/target_genomes_gtdb.txt
[2023-03-15 09:50:08,019] [INFO] Task started: fastANI
[2023-03-15 09:50:08,020] [INFO] Running command: fastANI --query /var/lib/cwl/stgb06c5b46-f386-447d-8198-5c2cf08ca0cd/OceanDNA-b39168.fa --refList OceanDNA-b39168/target_genomes_gtdb.txt --output OceanDNA-b39168/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:50:22,702] [INFO] Task succeeded: fastANI
[2023-03-15 09:50:22,716] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:50:22,716] [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
GCA_002717955.1	s__Marinobacter_A sp002717955	99.9876	1290	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	99.94	99.88	0.97	0.95	4	conclusive
GCF_003789045.1	s__Marinobacter_A sp003789045	78.1699	441	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCF_003258515.1	s__Marinobacter_A bohaiensis	78.1129	419	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
GCF_008122265.1	s__Marinobacter_A fonticola	78.0878	394	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327985.1	s__Marinobacter_A halodurans	78.0461	434	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364845.1	s__Marinobacter_A nanhaiticus	78.0223	382	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170835.1	s__Marinobacter algicola	77.8441	249	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359475.1	s__Marinobacter sp014359475	77.7725	205	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114775.1	s__Marinobacter zhejiangensis	77.6087	215	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344045.1	s__Marinobacter vulgaris	77.5605	214	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	77.4848	248	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193265.1	s__Marinobacter changyiensis	77.4496	224	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	77.4451	251	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860765.1	s__Marinobacter salexigens_A	77.4044	138	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686085.1	s__Marinobacter sp000686085	77.3798	246	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002933275.1	s__Marinobacter maroccanus	77.31	242	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744715.1	s__Marinobacter profundi	77.2512	276	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCF_900114925.1	s__Marinobacter pelagius	77.2497	235	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792665.1	s__Marinobacter orientalis	77.0745	201	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014762755.1	s__Marinobacter sp014762755	77.0499	166	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:50:23,010] [INFO] GTDB search result was written to OceanDNA-b39168/result_gtdb.tsv
[2023-03-15 09:50:23,071] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:50:23,074] [INFO] DFAST_QC result json was written to OceanDNA-b39168/dqc_result.json
[2023-03-15 09:50:23,074] [INFO] DFAST_QC completed!
[2023-03-15 09:50:23,074] [INFO] Total running time: 0h2m4s