[2024-01-25 18:49:20,497] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:20,499] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:20,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg67828994-0bd8-4a4f-88d2-d058d639d8dd/dqc_reference
[2024-01-25 18:49:21,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:21,638] [INFO] Task started: Prodigal
[2024-01-25 18:49:21,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c1a5bb9-46ca-4e88-8c7c-1cf68510640e/GCF_003025495.1_ASM302549v1_genomic.fna.gz | prodigal -d GCF_003025495.1_ASM302549v1_genomic.fna/cds.fna -a GCF_003025495.1_ASM302549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:32,387] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:32,387] [INFO] Task started: HMMsearch
[2024-01-25 18:49:32,387] [INFO] Running command: hmmsearch --tblout GCF_003025495.1_ASM302549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67828994-0bd8-4a4f-88d2-d058d639d8dd/dqc_reference/reference_markers.hmm GCF_003025495.1_ASM302549v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:32,664] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:32,665] [INFO] Found 6/6 markers.
[2024-01-25 18:49:32,708] [INFO] Query marker FASTA was written to GCF_003025495.1_ASM302549v1_genomic.fna/markers.fasta
[2024-01-25 18:49:32,709] [INFO] Task started: Blastn
[2024-01-25 18:49:32,709] [INFO] Running command: blastn -query GCF_003025495.1_ASM302549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67828994-0bd8-4a4f-88d2-d058d639d8dd/dqc_reference/reference_markers.fasta -out GCF_003025495.1_ASM302549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:33,488] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:33,491] [INFO] Selected 16 target genomes.
[2024-01-25 18:49:33,491] [INFO] Target genome list was writen to GCF_003025495.1_ASM302549v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:33,499] [INFO] Task started: fastANI
[2024-01-25 18:49:33,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c1a5bb9-46ca-4e88-8c7c-1cf68510640e/GCF_003025495.1_ASM302549v1_genomic.fna.gz --refList GCF_003025495.1_ASM302549v1_genomic.fna/target_genomes.txt --output GCF_003025495.1_ASM302549v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:48,602] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:48,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67828994-0bd8-4a4f-88d2-d058d639d8dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:48,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67828994-0bd8-4a4f-88d2-d058d639d8dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:48,613] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:49:48,613] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:48,613] [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
Photobacterium jeanii	strain=DSM 100339	GCA_003025495.1	858640	858640	type	True	100.0	1664	1666	95	conclusive
Photobacterium jeanii	strain=R-40508	GCA_001650345.1	858640	858640	type	True	99.9927	1650	1666	95	conclusive
Photobacterium swingsii	strain=DSM 24669	GCA_003026435.1	680026	680026	type	True	81.8624	960	1666	95	below_threshold
Photobacterium swingsii	strain=CAIM 1393	GCA_001077885.1	680026	680026	type	True	81.7583	934	1666	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	81.7068	960	1666	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	81.2212	950	1666	95	below_threshold
Photobacterium sanguinicancri	strain=CAIM 1827	GCA_002265265.1	875932	875932	type	True	81.1636	869	1666	95	below_threshold
Photobacterium rosenbergii	strain=DSM 19138	GCA_003026455.1	294936	294936	type	True	79.9367	441	1666	95	below_threshold
Photobacterium leiognathi	strain=ATCC 25521	GCA_003026235.1	553611	553611	type	True	79.7957	393	1666	95	below_threshold
Photobacterium lucens	strain=CAIM 1937	GCA_009873615.1	2562949	2562949	type	True	79.7306	381	1666	95	below_threshold
Photobacterium leiognathi	strain=ATCC 25521	GCA_000950415.1	553611	553611	type	True	79.7269	397	1666	95	below_threshold
Photobacterium proteolyticum	strain=13-12	GCA_001939735.1	1903952	1903952	type	True	79.6232	433	1666	95	below_threshold
Photobacterium alginatilyticum	strain=P03D4	GCA_009910675.1	1775171	1775171	type	True	79.5363	432	1666	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.9374	212	1666	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.9256	221	1666	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	77.5427	207	1666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:48,619] [INFO] DFAST Taxonomy check result was written to GCF_003025495.1_ASM302549v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:48,622] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:48,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:48,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67828994-0bd8-4a4f-88d2-d058d639d8dd/dqc_reference/checkm_data
[2024-01-25 18:49:48,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:48,685] [INFO] Task started: CheckM
[2024-01-25 18:49:48,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003025495.1_ASM302549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003025495.1_ASM302549v1_genomic.fna/checkm_input GCF_003025495.1_ASM302549v1_genomic.fna/checkm_result
[2024-01-25 18:50:23,721] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:23,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:23,742] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:23,742] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:23,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003025495.1_ASM302549v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:23,744] [INFO] Task started: Blastn
[2024-01-25 18:50:23,744] [INFO] Running command: blastn -query GCF_003025495.1_ASM302549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67828994-0bd8-4a4f-88d2-d058d639d8dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003025495.1_ASM302549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:24,946] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:24,949] [INFO] Selected 16 target genomes.
[2024-01-25 18:50:24,949] [INFO] Target genome list was writen to GCF_003025495.1_ASM302549v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:24,967] [INFO] Task started: fastANI
[2024-01-25 18:50:24,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c1a5bb9-46ca-4e88-8c7c-1cf68510640e/GCF_003025495.1_ASM302549v1_genomic.fna.gz --refList GCF_003025495.1_ASM302549v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003025495.1_ASM302549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:40,811] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:40,822] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:40,822] [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_001650345.1	s__Photobacterium jeanii	99.9927	1650	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001077885.1	s__Photobacterium swingsii	81.7542	936	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002265265.1	s__Photobacterium sanguinicancri	81.1766	866	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.87	97.87	0.90	0.90	2	-
GCF_003026455.1	s__Photobacterium rosenbergii	79.9485	440	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_000940995.1	s__Photobacterium gaetbulicola	79.7968	399	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.90	95.81	0.93	0.87	3	-
GCF_000950415.1	s__Photobacterium leiognathi	79.7172	397	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.11	96.59	0.91	0.88	15	-
GCF_003026495.1	s__Photobacterium sanctipauli	79.7163	473	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009873615.1	s__Photobacterium lucens	79.7121	383	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.83	97.58	0.96	0.94	5	-
GCF_000331515.1	s__Photobacterium marinum	79.6294	433	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_001939735.1	s__Photobacterium proteolyticum	79.6111	434	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001029435.1	s__Photobacterium aphoticum	79.5524	459	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.09	97.29	0.97	0.93	4	-
GCF_009910675.1	s__Photobacterium alginatilyticum	79.5193	432	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026475.1	s__Photobacterium lipolyticum	79.0712	434	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954725.1	s__Photobacterium phosphoreum	79.0317	282	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.41	96.65	0.93	0.88	23	-
GCF_003026395.1	s__Photobacterium iliopiscarium	78.6017	304	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.31	98.95	0.95	0.91	7	-
GCF_000695255.1	s__Photobacterium galatheae	78.5294	176	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:40,824] [INFO] GTDB search result was written to GCF_003025495.1_ASM302549v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:40,824] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:40,827] [INFO] DFAST_QC result json was written to GCF_003025495.1_ASM302549v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:40,828] [INFO] DFAST_QC completed!
[2024-01-25 18:50:40,828] [INFO] Total running time: 0h1m20s