[2024-01-24 14:39:01,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:01,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:01,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b89dd89-aae4-49cb-a7bb-5cd181dec728/dqc_reference
[2024-01-24 14:39:04,246] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,247] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,247] [INFO] Running command: gunzip -c /var/lib/cwl/stgd687ce4e-763b-4fd4-bf48-e2099eed91b5/GCF_003762925.1_ASM376292v1_genomic.fna.gz | prodigal -d GCF_003762925.1_ASM376292v1_genomic.fna/cds.fna -a GCF_003762925.1_ASM376292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:16,134] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:16,134] [INFO] Task started: HMMsearch
[2024-01-24 14:39:16,134] [INFO] Running command: hmmsearch --tblout GCF_003762925.1_ASM376292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b89dd89-aae4-49cb-a7bb-5cd181dec728/dqc_reference/reference_markers.hmm GCF_003762925.1_ASM376292v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:16,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:16,433] [INFO] Found 6/6 markers.
[2024-01-24 14:39:16,484] [INFO] Query marker FASTA was written to GCF_003762925.1_ASM376292v1_genomic.fna/markers.fasta
[2024-01-24 14:39:16,485] [INFO] Task started: Blastn
[2024-01-24 14:39:16,485] [INFO] Running command: blastn -query GCF_003762925.1_ASM376292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b89dd89-aae4-49cb-a7bb-5cd181dec728/dqc_reference/reference_markers.fasta -out GCF_003762925.1_ASM376292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:17,348] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:17,351] [INFO] Selected 24 target genomes.
[2024-01-24 14:39:17,352] [INFO] Target genome list was writen to GCF_003762925.1_ASM376292v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:17,361] [INFO] Task started: fastANI
[2024-01-24 14:39:17,361] [INFO] Running command: fastANI --query /var/lib/cwl/stgd687ce4e-763b-4fd4-bf48-e2099eed91b5/GCF_003762925.1_ASM376292v1_genomic.fna.gz --refList GCF_003762925.1_ASM376292v1_genomic.fna/target_genomes.txt --output GCF_003762925.1_ASM376292v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:35,011] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:35,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b89dd89-aae4-49cb-a7bb-5cd181dec728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:35,012] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b89dd89-aae4-49cb-a7bb-5cd181dec728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:35,028] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:35,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:35,029] [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
Marinimicrobium koreense	strain=DSM 16974	GCA_003762925.1	306545	306545	type	True	100.0	1279	1279	95	conclusive
Marinimicrobium agarilyticum	strain=DSM 16975	GCA_000423345.1	306546	306546	type	True	80.2563	660	1279	95	below_threshold
Marinimicrobium alkaliphilum	strain=SW121	GCA_003259155.1	2202654	2202654	type	True	77.7694	294	1279	95	below_threshold
Microbulbifer rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	77.6292	156	1279	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	77.4616	136	1279	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	77.4498	124	1279	95	below_threshold
Microbulbifer yueqingensis	strain=CGMCC 1.10658	GCA_900100355.1	658219	658219	type	True	77.3662	141	1279	95	below_threshold
Microbulbifer flavimaris	strain=WRN-8	GCA_001641755.2	1781068	1781068	type	True	77.3661	135	1279	95	below_threshold
Simiduia agarivorans	strain=SA1 = DSM 21679	GCA_000305785.2	447471	447471	type	True	77.2743	120	1279	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	77.1779	156	1279	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	77.1707	162	1279	95	below_threshold
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	77.1276	124	1279	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.1197	92	1279	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	76.9839	117	1279	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.9336	89	1279	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.7749	90	1279	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.7345	101	1279	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	76.7212	86	1279	95	below_threshold
Saccharospirillum salsuginis	strain=KCTC 22169	GCA_014651855.1	418750	418750	type	True	76.6851	100	1279	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.6042	99	1279	95	below_threshold
Exilibacterium tricleocarpae	strain=R142	GCA_007004655.1	2591008	2591008	type	True	76.4248	123	1279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:35,030] [INFO] DFAST Taxonomy check result was written to GCF_003762925.1_ASM376292v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:35,031] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:35,031] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:35,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b89dd89-aae4-49cb-a7bb-5cd181dec728/dqc_reference/checkm_data
[2024-01-24 14:39:35,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:35,077] [INFO] Task started: CheckM
[2024-01-24 14:39:35,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003762925.1_ASM376292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003762925.1_ASM376292v1_genomic.fna/checkm_input GCF_003762925.1_ASM376292v1_genomic.fna/checkm_result
[2024-01-24 14:40:13,771] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:13,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:13,790] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:13,790] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:13,790] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003762925.1_ASM376292v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:13,790] [INFO] Task started: Blastn
[2024-01-24 14:40:13,791] [INFO] Running command: blastn -query GCF_003762925.1_ASM376292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b89dd89-aae4-49cb-a7bb-5cd181dec728/dqc_reference/reference_markers_gtdb.fasta -out GCF_003762925.1_ASM376292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:15,122] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:15,125] [INFO] Selected 21 target genomes.
[2024-01-24 14:40:15,125] [INFO] Target genome list was writen to GCF_003762925.1_ASM376292v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:15,139] [INFO] Task started: fastANI
[2024-01-24 14:40:15,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgd687ce4e-763b-4fd4-bf48-e2099eed91b5/GCF_003762925.1_ASM376292v1_genomic.fna.gz --refList GCF_003762925.1_ASM376292v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003762925.1_ASM376292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:30,560] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:30,575] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:30,575] [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_003762925.1	s__Marinimicrobium koreense	100.0	1279	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	96.56	95.81	0.88	0.87	5	conclusive
GCF_000423345.1	s__Marinimicrobium agarilyticum	80.2566	660	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259155.1	s__Marinimicrobium_A alkaliphilum	77.7841	292	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191725.1	s__Microbulbifer rhizosphaerae	77.6292	156	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750105.1	s__Microbulbifer aggregans	77.4804	132	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377745.1	s__Gilvimarinus chinensis	77.4259	125	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641755.2	s__Microbulbifer flavimaris	77.3528	135	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009857815.1	s__Pseudomaricurvus sp009857815	77.3381	155	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000305785.2	s__Simiduia agarivorans	77.2743	120	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Simiduia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900129095.1	s__Microbulbifer donghaiensis	77.1707	162	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904815.1	s__Microbulbifer taiwanensis	77.16	155	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015182315.1	s__Cellvibrio polysaccharolyticus	77.1276	124	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009903625.1	s__Microbulbifer sp009903625	77.1053	163	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019225.1	s__Cellvibrio japonicus	76.9394	139	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	100.00	100.00	1.00	1.00	4	-
GCA_003634075.1	s__Teredinibacter sp003634075	76.571	142	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004655.1	s__Exilibacterium tricleocarpae	76.4533	124	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Exilibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005491205.1	s__Chimaeribacter sp005491205	76.1841	69	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chimaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483145.1	s__Cellvibrio sp002483145	75.9917	75	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:30,577] [INFO] GTDB search result was written to GCF_003762925.1_ASM376292v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:30,578] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:30,581] [INFO] DFAST_QC result json was written to GCF_003762925.1_ASM376292v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:30,582] [INFO] DFAST_QC completed!
[2024-01-24 14:40:30,582] [INFO] Total running time: 0h1m29s