[2024-01-24 14:13:18,452] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:18,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:18,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d60f89f-f96d-4005-ba80-456e6ed59248/dqc_reference
[2024-01-24 14:13:19,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:19,854] [INFO] Task started: Prodigal
[2024-01-24 14:13:19,854] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1208099-6cc1-4904-96d0-cdb48315781b/GCF_030409605.1_ASM3040960v1_genomic.fna.gz | prodigal -d GCF_030409605.1_ASM3040960v1_genomic.fna/cds.fna -a GCF_030409605.1_ASM3040960v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:32,884] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:32,884] [INFO] Task started: HMMsearch
[2024-01-24 14:13:32,884] [INFO] Running command: hmmsearch --tblout GCF_030409605.1_ASM3040960v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d60f89f-f96d-4005-ba80-456e6ed59248/dqc_reference/reference_markers.hmm GCF_030409605.1_ASM3040960v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:33,256] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:33,257] [INFO] Found 6/6 markers.
[2024-01-24 14:13:33,296] [INFO] Query marker FASTA was written to GCF_030409605.1_ASM3040960v1_genomic.fna/markers.fasta
[2024-01-24 14:13:33,296] [INFO] Task started: Blastn
[2024-01-24 14:13:33,297] [INFO] Running command: blastn -query GCF_030409605.1_ASM3040960v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d60f89f-f96d-4005-ba80-456e6ed59248/dqc_reference/reference_markers.fasta -out GCF_030409605.1_ASM3040960v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:34,038] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:34,041] [INFO] Selected 32 target genomes.
[2024-01-24 14:13:34,041] [INFO] Target genome list was writen to GCF_030409605.1_ASM3040960v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:34,058] [INFO] Task started: fastANI
[2024-01-24 14:13:34,059] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1208099-6cc1-4904-96d0-cdb48315781b/GCF_030409605.1_ASM3040960v1_genomic.fna.gz --refList GCF_030409605.1_ASM3040960v1_genomic.fna/target_genomes.txt --output GCF_030409605.1_ASM3040960v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:54,475] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:54,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d60f89f-f96d-4005-ba80-456e6ed59248/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:54,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d60f89f-f96d-4005-ba80-456e6ed59248/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:54,493] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:54,494] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:54,494] [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
Simiduia aestuariiviva	strain=CECT 8571	GCA_014192475.1	1510459	1510459	type	True	78.2846	320	1511	95	below_threshold
Simiduia agarivorans	strain=SA1 = DSM 21679	GCA_000305785.2	447471	447471	type	True	78.0403	285	1511	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	77.7975	274	1511	95	below_threshold
Teredinibacter haidensis	strain=Bs08	GCA_014211975.1	2731755	2731755	type	True	77.6737	51	1511	95	below_threshold
Saccharophagus degradans	strain=2-40	GCA_000013665.1	86304	86304	type	True	77.6601	63	1511	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	76.8922	56	1511	95	below_threshold
Cellvibrio zantedeschiae	strain=KCTC 32239	GCA_014652535.1	1237077	1237077	type	True	76.6212	56	1511	95	below_threshold
Aestuariicella hydrocarbonica	strain=JCM 30134	GCA_011602365.1	1470433	1470433	type	True	76.5176	65	1511	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	76.2744	65	1511	95	below_threshold
Gilvimarinus polysaccharolyticus	strain=YN3	GCA_001187555.1	863921	863921	type	True	76.2513	66	1511	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	76.2068	52	1511	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	76.0712	74	1511	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	75.5267	56	1511	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:54,496] [INFO] DFAST Taxonomy check result was written to GCF_030409605.1_ASM3040960v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:54,498] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:54,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:54,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d60f89f-f96d-4005-ba80-456e6ed59248/dqc_reference/checkm_data
[2024-01-24 14:13:54,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:54,547] [INFO] Task started: CheckM
[2024-01-24 14:13:54,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409605.1_ASM3040960v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409605.1_ASM3040960v1_genomic.fna/checkm_input GCF_030409605.1_ASM3040960v1_genomic.fna/checkm_result
[2024-01-24 14:14:33,513] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:33,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:33,538] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:33,538] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:33,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409605.1_ASM3040960v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:33,539] [INFO] Task started: Blastn
[2024-01-24 14:14:33,539] [INFO] Running command: blastn -query GCF_030409605.1_ASM3040960v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d60f89f-f96d-4005-ba80-456e6ed59248/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409605.1_ASM3040960v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:34,461] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:34,466] [INFO] Selected 31 target genomes.
[2024-01-24 14:14:34,466] [INFO] Target genome list was writen to GCF_030409605.1_ASM3040960v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:34,498] [INFO] Task started: fastANI
[2024-01-24 14:14:34,499] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1208099-6cc1-4904-96d0-cdb48315781b/GCF_030409605.1_ASM3040960v1_genomic.fna.gz --refList GCF_030409605.1_ASM3040960v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409605.1_ASM3040960v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:54,014] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:54,025] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:14:54,025] [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_014192475.1	s__Simiduia aestuariiviva	78.2726	321	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Simiduia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000305785.2	s__Simiduia agarivorans	78.0462	285	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Simiduia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001183545.1	s__Cellvibrio sp001183545	77.7407	65	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013665.1	s__Saccharophagus degradans	77.7163	63	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Saccharophagus	95.0	96.22	96.22	0.89	0.89	2	-
GCF_014211975.1	s__Teredinibacter haidensis	77.5996	50	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000832015.1	s__Gilvimarinus agarilyticus	77.2611	82	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857815.1	s__Pseudomaricurvus sp009857815	76.692	62	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602365.1	s__Pseudomaricurvus hydrocarbonicus	76.4881	66	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129095.1	s__Microbulbifer donghaiensis	76.186	64	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004172865.1	s__Cellvibrio sp004172865	76.1109	53	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863235.1	s__Pseudomaricurvus sp018863235	76.1009	74	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904815.1	s__Microbulbifer taiwanensis	76.072	58	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303155.1	s__Microbulbifer salipaludis	75.7176	60	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:54,027] [INFO] GTDB search result was written to GCF_030409605.1_ASM3040960v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:54,027] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:54,037] [INFO] DFAST_QC result json was written to GCF_030409605.1_ASM3040960v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:54,037] [INFO] DFAST_QC completed!
[2024-01-24 14:14:54,037] [INFO] Total running time: 0h1m36s