[2024-01-24 12:30:49,358] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:49,360] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:49,360] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6496388-7604-4810-a353-6f94ace981f0/dqc_reference
[2024-01-24 12:30:50,556] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:50,557] [INFO] Task started: Prodigal
[2024-01-24 12:30:50,557] [INFO] Running command: gunzip -c /var/lib/cwl/stg545b01ce-fe7b-4550-8882-0396aabe5ca0/GCF_009193265.1_ASM919326v1_genomic.fna.gz | prodigal -d GCF_009193265.1_ASM919326v1_genomic.fna/cds.fna -a GCF_009193265.1_ASM919326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:03,251] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:03,252] [INFO] Task started: HMMsearch
[2024-01-24 12:31:03,252] [INFO] Running command: hmmsearch --tblout GCF_009193265.1_ASM919326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6496388-7604-4810-a353-6f94ace981f0/dqc_reference/reference_markers.hmm GCF_009193265.1_ASM919326v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:03,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:03,535] [INFO] Found 6/6 markers.
[2024-01-24 12:31:03,597] [INFO] Query marker FASTA was written to GCF_009193265.1_ASM919326v1_genomic.fna/markers.fasta
[2024-01-24 12:31:03,598] [INFO] Task started: Blastn
[2024-01-24 12:31:03,598] [INFO] Running command: blastn -query GCF_009193265.1_ASM919326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6496388-7604-4810-a353-6f94ace981f0/dqc_reference/reference_markers.fasta -out GCF_009193265.1_ASM919326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:04,385] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:04,390] [INFO] Selected 24 target genomes.
[2024-01-24 12:31:04,390] [INFO] Target genome list was writen to GCF_009193265.1_ASM919326v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:04,398] [INFO] Task started: fastANI
[2024-01-24 12:31:04,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg545b01ce-fe7b-4550-8882-0396aabe5ca0/GCF_009193265.1_ASM919326v1_genomic.fna.gz --refList GCF_009193265.1_ASM919326v1_genomic.fna/target_genomes.txt --output GCF_009193265.1_ASM919326v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:21,498] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:21,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6496388-7604-4810-a353-6f94ace981f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:21,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6496388-7604-4810-a353-6f94ace981f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:21,528] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:21,529] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:21,529] [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 changyiensis	strain=CLL7-20	GCA_009193265.1	2604091	2604091	type	True	100.0	1440	1441	95	conclusive
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	79.5055	457	1441	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	78.9533	431	1441	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.7072	399	1441	95	below_threshold
Marinobacter salicampi	strain=ISL-40	GCA_011074795.1	435907	435907	type	True	78.6843	391	1441	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	78.5718	347	1441	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	78.4154	315	1441	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.3495	365	1441	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	78.3187	368	1441	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.2617	353	1441	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	78.1286	292	1441	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	78.1281	356	1441	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	78.0947	338	1441	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	78.0714	301	1441	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	77.9665	337	1441	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.9249	290	1441	95	below_threshold
Marinobacter confluentis	strain=KCTC 42705	GCA_008795935.1	1697557	1697557	type	True	77.863	336	1441	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	77.838	280	1441	95	below_threshold
Marinobacter gelidimuriae	strain=BF04_CF-4	GCA_000372805.1	2739064	2739064	type	True	77.8257	184	1441	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	77.7809	283	1441	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	77.7305	304	1441	95	below_threshold
Marinobacter nitratireducens	strain=AK21	GCA_000708045.1	1137280	1137280	type	True	77.7304	266	1441	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	77.6097	308	1441	95	below_threshold
Marinobacter psychrophilus	strain=20041	GCA_001043175.1	330734	330734	type	True	77.5422	183	1441	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:21,530] [INFO] DFAST Taxonomy check result was written to GCF_009193265.1_ASM919326v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:21,531] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:21,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:21,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6496388-7604-4810-a353-6f94ace981f0/dqc_reference/checkm_data
[2024-01-24 12:31:21,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:21,574] [INFO] Task started: CheckM
[2024-01-24 12:31:21,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009193265.1_ASM919326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009193265.1_ASM919326v1_genomic.fna/checkm_input GCF_009193265.1_ASM919326v1_genomic.fna/checkm_result
[2024-01-24 12:32:01,165] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:01,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:01,187] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:01,187] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:01,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009193265.1_ASM919326v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:01,188] [INFO] Task started: Blastn
[2024-01-24 12:32:01,188] [INFO] Running command: blastn -query GCF_009193265.1_ASM919326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6496388-7604-4810-a353-6f94ace981f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_009193265.1_ASM919326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:02,486] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:02,490] [INFO] Selected 24 target genomes.
[2024-01-24 12:32:02,491] [INFO] Target genome list was writen to GCF_009193265.1_ASM919326v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:02,518] [INFO] Task started: fastANI
[2024-01-24 12:32:02,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg545b01ce-fe7b-4550-8882-0396aabe5ca0/GCF_009193265.1_ASM919326v1_genomic.fna.gz --refList GCF_009193265.1_ASM919326v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009193265.1_ASM919326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:20,343] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:20,366] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:20,366] [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_009193265.1	s__Marinobacter changyiensis	100.0	1440	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005298175.1	s__Marinobacter sp005298175	79.7431	465	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011074955.1	s__Marinobacter caseinilyticus	79.5167	456	1441	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	78.9333	433	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008795955.1	s__Marinobacter sp008795955	78.7125	399	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011074795.1	s__Marinobacter salicampi	78.711	389	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994855.1	s__Marinobacter sp003994855	78.5676	369	1441	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	78.5648	421	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003007685.1	s__Marinobacter halophilus	78.4071	317	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009617755.1	s__Marinobacter salsuginis	78.3662	348	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	78.2937	356	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCA_017643965.1	s__Marinobacter sp017643965	78.1838	272	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169375.1	s__Marinobacter sp000169375	78.1824	212	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007715.1	s__Marinobacter shengliensis	78.1082	295	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
GCF_001447155.2	s__Marinobacter sp001447155	78.0914	301	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	78.088	342	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402255.1	s__Marinobacter sp018402255	78.0202	280	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.33	99.33	0.88	0.88	2	-
GCF_004785685.1	s__Marinobacter confluentis	77.8539	343	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	77.8527	307	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCA_002726615.1	s__Marinobacter sp002726615	77.8275	252	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.52	98.30	0.75	0.64	3	-
GCF_000372805.1	s__Marinobacter gelidimuriae	77.8071	185	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327985.1	s__Marinobacter_A halodurans	77.7766	285	1441	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_000708045.1	s__Marinobacter nitratireducens	77.7272	267	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.86	98.83	0.90	0.89	3	-
GCF_003258515.1	s__Marinobacter_A bohaiensis	77.6001	309	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:20,368] [INFO] GTDB search result was written to GCF_009193265.1_ASM919326v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:20,368] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:20,373] [INFO] DFAST_QC result json was written to GCF_009193265.1_ASM919326v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:20,373] [INFO] DFAST_QC completed!
[2024-01-24 12:32:20,373] [INFO] Total running time: 0h1m31s