[2024-01-24 13:57:27,643] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:27,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:27,645] [INFO] DQC Reference Directory: /var/lib/cwl/stga5d3643d-28b0-4111-af7e-104e055ae08e/dqc_reference
[2024-01-24 13:57:28,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:28,911] [INFO] Task started: Prodigal
[2024-01-24 13:57:28,912] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf976c98-25b6-43b7-ae0c-7b719c2123bf/GCF_001939735.1_ASM193973v1_genomic.fna.gz | prodigal -d GCF_001939735.1_ASM193973v1_genomic.fna/cds.fna -a GCF_001939735.1_ASM193973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:45,666] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:45,666] [INFO] Task started: HMMsearch
[2024-01-24 13:57:45,667] [INFO] Running command: hmmsearch --tblout GCF_001939735.1_ASM193973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5d3643d-28b0-4111-af7e-104e055ae08e/dqc_reference/reference_markers.hmm GCF_001939735.1_ASM193973v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:46,043] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:46,045] [INFO] Found 6/6 markers.
[2024-01-24 13:57:46,100] [INFO] Query marker FASTA was written to GCF_001939735.1_ASM193973v1_genomic.fna/markers.fasta
[2024-01-24 13:57:46,100] [INFO] Task started: Blastn
[2024-01-24 13:57:46,100] [INFO] Running command: blastn -query GCF_001939735.1_ASM193973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5d3643d-28b0-4111-af7e-104e055ae08e/dqc_reference/reference_markers.fasta -out GCF_001939735.1_ASM193973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:46,927] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:46,931] [INFO] Selected 19 target genomes.
[2024-01-24 13:57:46,931] [INFO] Target genome list was writen to GCF_001939735.1_ASM193973v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:46,937] [INFO] Task started: fastANI
[2024-01-24 13:57:46,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf976c98-25b6-43b7-ae0c-7b719c2123bf/GCF_001939735.1_ASM193973v1_genomic.fna.gz --refList GCF_001939735.1_ASM193973v1_genomic.fna/target_genomes.txt --output GCF_001939735.1_ASM193973v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:07,176] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:07,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5d3643d-28b0-4111-af7e-104e055ae08e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:07,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5d3643d-28b0-4111-af7e-104e055ae08e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:07,192] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:07,192] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:07,192] [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 proteolyticum	strain=13-12	GCA_001939735.1	1903952	1903952	type	True	100.0	2110	2113	95	conclusive
Photobacterium alginatilyticum	strain=P03D4	GCA_009910675.1	1775171	1775171	type	True	93.7725	1769	2113	95	below_threshold
Photobacterium chitinilyticum	strain=BEI247	GCA_004104355.1	2485123	2485123	type	True	83.4864	1331	2113	95	below_threshold
Photobacterium marinum	strain=AK15	GCA_000331515.1	1056511	1056511	type	True	80.6687	761	2113	95	below_threshold
Photobacterium sanctipauli	strain=A-394	GCA_000730475.1	1342794	1342794	type	True	80.3996	459	2113	95	below_threshold
Photobacterium sanctipauli	strain=DSM 100436	GCA_003026495.1	1342794	1342794	type	True	80.3256	617	2113	95	below_threshold
Photobacterium rosenbergii	strain=DSM 19138	GCA_003026455.1	294936	294936	type	True	80.1478	591	2113	95	below_threshold
Photobacterium aphoticum	strain=DSM 25995	GCA_003025575.1	754436	754436	type	True	79.9612	470	2113	95	below_threshold
Photobacterium jeanii	strain=DSM 100339	GCA_003025495.1	858640	858640	type	True	79.6934	443	2113	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.6859	420	2113	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	79.5797	537	2113	95	below_threshold
Photobacterium jeanii	strain=R-40508	GCA_001650345.1	858640	858640	type	True	79.5608	443	2113	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.5406	437	2113	95	below_threshold
Photobacterium aquae	strain=CGMCC 1.12159	GCA_001029445.1	1195763	1195763	type	True	79.539	527	2113	95	below_threshold
Photobacterium ganghwense	strain=DSM 22954	GCA_001029455.1	320778	320778	type	True	79.463	546	2113	95	below_threshold
Photobacterium swingsii	strain=CAIM 1393	GCA_001077885.1	680026	680026	type	True	79.3449	435	2113	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	78.6376	174	2113	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	77.7284	191	2113	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	76.2941	91	2113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:07,194] [INFO] DFAST Taxonomy check result was written to GCF_001939735.1_ASM193973v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:07,195] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:07,195] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:07,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5d3643d-28b0-4111-af7e-104e055ae08e/dqc_reference/checkm_data
[2024-01-24 13:58:07,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:07,254] [INFO] Task started: CheckM
[2024-01-24 13:58:07,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001939735.1_ASM193973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001939735.1_ASM193973v1_genomic.fna/checkm_input GCF_001939735.1_ASM193973v1_genomic.fna/checkm_result
[2024-01-24 13:58:59,329] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:59,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:59,349] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:59,349] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:59,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001939735.1_ASM193973v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:59,349] [INFO] Task started: Blastn
[2024-01-24 13:58:59,350] [INFO] Running command: blastn -query GCF_001939735.1_ASM193973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5d3643d-28b0-4111-af7e-104e055ae08e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001939735.1_ASM193973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:00,760] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:00,764] [INFO] Selected 12 target genomes.
[2024-01-24 13:59:00,764] [INFO] Target genome list was writen to GCF_001939735.1_ASM193973v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:00,777] [INFO] Task started: fastANI
[2024-01-24 13:59:00,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf976c98-25b6-43b7-ae0c-7b719c2123bf/GCF_001939735.1_ASM193973v1_genomic.fna.gz --refList GCF_001939735.1_ASM193973v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001939735.1_ASM193973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:15,666] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:15,679] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:15,679] [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_001939735.1	s__Photobacterium proteolyticum	100.0	2110	2113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009910675.1	s__Photobacterium alginatilyticum	93.769	1770	2113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104355.1	s__Photobacterium chitinilyticum	83.4928	1329	2113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331515.1	s__Photobacterium marinum	80.6524	763	2113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_003026495.1	s__Photobacterium sanctipauli	80.3302	618	2113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026455.1	s__Photobacterium rosenbergii	80.1206	594	2113	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	80.1061	620	2113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.90	95.81	0.93	0.87	3	-
GCF_001029435.1	s__Photobacterium aphoticum	79.8345	488	2113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.09	97.29	0.97	0.93	4	-
GCF_003025595.1	s__Photobacterium ganghwense	79.5704	538	2113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.50	98.82	0.97	0.96	4	-
GCF_001650345.1	s__Photobacterium jeanii	79.5642	442	2113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001029445.1	s__Photobacterium aquae	79.5339	528	2113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001077885.1	s__Photobacterium swingsii	79.3414	437	2113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:15,682] [INFO] GTDB search result was written to GCF_001939735.1_ASM193973v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:15,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:15,687] [INFO] DFAST_QC result json was written to GCF_001939735.1_ASM193973v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:15,687] [INFO] DFAST_QC completed!
[2024-01-24 13:59:15,687] [INFO] Total running time: 0h1m48s