[2023-03-17 07:01:49,601] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,601] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,602] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc193863-44f2-4910-bf96-ca1b05a9f421/dqc_reference
[2023-03-17 07:01:51,531] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:51,531] [INFO] Task started: Prodigal
[2023-03-17 07:01:51,531] [INFO] Running command: cat /var/lib/cwl/stg6043e146-c8c3-47d8-a075-f92246663545/OceanDNA-b34729.fa | prodigal -d OceanDNA-b34729/cds.fna -a OceanDNA-b34729/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:02:20,203] [INFO] Task succeeded: Prodigal
[2023-03-17 07:02:20,203] [INFO] Task started: HMMsearch
[2023-03-17 07:02:20,203] [INFO] Running command: hmmsearch --tblout OceanDNA-b34729/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc193863-44f2-4910-bf96-ca1b05a9f421/dqc_reference/reference_markers.hmm OceanDNA-b34729/protein.faa > /dev/null
[2023-03-17 07:02:20,444] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:02:20,445] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6043e146-c8c3-47d8-a075-f92246663545/OceanDNA-b34729.fa]
[2023-03-17 07:02:20,475] [INFO] Query marker FASTA was written to OceanDNA-b34729/markers.fasta
[2023-03-17 07:02:20,475] [INFO] Task started: Blastn
[2023-03-17 07:02:20,475] [INFO] Running command: blastn -query OceanDNA-b34729/markers.fasta -db /var/lib/cwl/stgcc193863-44f2-4910-bf96-ca1b05a9f421/dqc_reference/reference_markers.fasta -out OceanDNA-b34729/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:20,991] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:20,992] [INFO] Selected 21 target genomes.
[2023-03-17 07:02:20,992] [INFO] Target genome list was writen to OceanDNA-b34729/target_genomes.txt
[2023-03-17 07:02:21,003] [INFO] Task started: fastANI
[2023-03-17 07:02:21,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg6043e146-c8c3-47d8-a075-f92246663545/OceanDNA-b34729.fa --refList OceanDNA-b34729/target_genomes.txt --output OceanDNA-b34729/fastani_result.tsv --threads 1
[2023-03-17 07:02:35,999] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:35,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc193863-44f2-4910-bf96-ca1b05a9f421/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:35,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc193863-44f2-4910-bf96-ca1b05a9f421/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:36,009] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:36,009] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:02:36,009] [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
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	78.3082	316	1819	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.9201	217	1819	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.8442	289	1819	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.7162	311	1819	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.6123	191	1819	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	77.3365	190	1819	95	below_threshold
Thalassomonas viridans	strain=XOM25	GCA_000948985.1	137584	137584	type	True	77.1793	88	1819	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	77.1084	196	1819	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	77.0782	197	1819	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	76.7857	170	1819	95	below_threshold
Thalassomonas actiniarum	strain=A5K-106	GCA_000948975.1	485447	485447	type	True	76.768	137	1819	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	76.7004	111	1819	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_002310815.1	314281	314281	type	True	75.9752	65	1819	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_000153245.1	314281	314281	type	True	75.9262	66	1819	95	below_threshold
Moritella dasanensis	strain=ArB 0140	GCA_000276805.1	428031	428031	type	True	75.8126	52	1819	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:02:36,009] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34729/tc_result.tsv
[2023-03-17 07:02:36,009] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:36,009] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:36,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc193863-44f2-4910-bf96-ca1b05a9f421/dqc_reference/checkm_data
[2023-03-17 07:02:36,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:36,020] [INFO] Task started: CheckM
[2023-03-17 07:02:36,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34729/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34729/checkm_input OceanDNA-b34729/checkm_result
[2023-03-17 07:03:44,868] [INFO] Task succeeded: CheckM
[2023-03-17 07:03:44,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:03:44,871] [INFO] ===== Completeness check finished =====
[2023-03-17 07:03:44,872] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:03:44,872] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34729/markers.fasta)
[2023-03-17 07:03:44,872] [INFO] Task started: Blastn
[2023-03-17 07:03:44,872] [INFO] Running command: blastn -query OceanDNA-b34729/markers.fasta -db /var/lib/cwl/stgcc193863-44f2-4910-bf96-ca1b05a9f421/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34729/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:03:45,532] [INFO] Task succeeded: Blastn
[2023-03-17 07:03:45,533] [INFO] Selected 18 target genomes.
[2023-03-17 07:03:45,533] [INFO] Target genome list was writen to OceanDNA-b34729/target_genomes_gtdb.txt
[2023-03-17 07:03:45,796] [INFO] Task started: fastANI
[2023-03-17 07:03:45,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg6043e146-c8c3-47d8-a075-f92246663545/OceanDNA-b34729.fa --refList OceanDNA-b34729/target_genomes_gtdb.txt --output OceanDNA-b34729/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:04:01,505] [INFO] Task succeeded: fastANI
[2023-03-17 07:04:01,516] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:04:01,516] [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_013215655.1	s__Colwellia_A sp013215655	99.0485	1616	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215295.1	s__Colwellia_A sp013215295	79.1687	431	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014076845.1	s__Colwellia_A sp014076845	78.4481	310	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
GCF_007954355.1	s__Colwellia_A hornerae	78.3432	312	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	100.00	100.00	0.99	0.99	3	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	78.089	311	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733765.1	s__Colwellia sp002733765	78.034	255	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCF_001767295.1	s__Colwellia_A sp001767295	78.0148	328	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	96.63	96.27	0.86	0.85	17	-
GCA_013215465.1	s__Colwellia sp013215465	77.9927	287	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCF_001440345.1	s__Colwellia sp001440345	77.9794	286	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	77.9615	272	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_002000085.1	s__Pseudocolwellia agarivorans	77.8257	289	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudocolwellia	95.0	95.36	95.36	0.90	0.90	2	-
GCF_002104475.1	s__Cognaticolwellia mytili	77.6987	312	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	77.6143	253	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491935.1	s__GCA-2401725 sp015491935	77.5207	217	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207645.1	s__Thalassotalea_B piscium	77.3365	190	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013216005.1	s__JABSOI01 sp013216005	77.3127	244	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487235.1	s__GCA-2401725 sp015487235	77.1536	203	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932965.1	s__Thalassotalea algicola	76.7469	171	1819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:04:01,516] [INFO] GTDB search result was written to OceanDNA-b34729/result_gtdb.tsv
[2023-03-17 07:04:01,516] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:04:01,518] [INFO] DFAST_QC result json was written to OceanDNA-b34729/dqc_result.json
[2023-03-17 07:04:01,518] [INFO] DFAST_QC completed!
[2023-03-17 07:04:01,518] [INFO] Total running time: 0h2m12s