[2024-01-24 13:22:00,995] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:00,999] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:00,999] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c1b387a-0995-413a-95a2-647032843841/dqc_reference
[2024-01-24 13:22:02,390] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:02,390] [INFO] Task started: Prodigal
[2024-01-24 13:22:02,391] [INFO] Running command: gunzip -c /var/lib/cwl/stg433ce11b-3956-4551-9ed7-2709ddde416c/GCF_900454585.1_49950_G01_genomic.fna.gz | prodigal -d GCF_900454585.1_49950_G01_genomic.fna/cds.fna -a GCF_900454585.1_49950_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:13,782] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:13,783] [INFO] Task started: HMMsearch
[2024-01-24 13:22:13,783] [INFO] Running command: hmmsearch --tblout GCF_900454585.1_49950_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c1b387a-0995-413a-95a2-647032843841/dqc_reference/reference_markers.hmm GCF_900454585.1_49950_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:14,126] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:14,128] [INFO] Found 6/6 markers.
[2024-01-24 13:22:14,169] [INFO] Query marker FASTA was written to GCF_900454585.1_49950_G01_genomic.fna/markers.fasta
[2024-01-24 13:22:14,170] [INFO] Task started: Blastn
[2024-01-24 13:22:14,170] [INFO] Running command: blastn -query GCF_900454585.1_49950_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c1b387a-0995-413a-95a2-647032843841/dqc_reference/reference_markers.fasta -out GCF_900454585.1_49950_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:14,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:14,982] [INFO] Selected 20 target genomes.
[2024-01-24 13:22:14,983] [INFO] Target genome list was writen to GCF_900454585.1_49950_G01_genomic.fna/target_genomes.txt
[2024-01-24 13:22:14,993] [INFO] Task started: fastANI
[2024-01-24 13:22:14,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg433ce11b-3956-4551-9ed7-2709ddde416c/GCF_900454585.1_49950_G01_genomic.fna.gz --refList GCF_900454585.1_49950_G01_genomic.fna/target_genomes.txt --output GCF_900454585.1_49950_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:38,973] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:38,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c1b387a-0995-413a-95a2-647032843841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:38,974] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c1b387a-0995-413a-95a2-647032843841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:38,989] [INFO] Found 20 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:22:38,990] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:38,990] [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 damselae	strain=NCTC11647	GCA_900454585.1	38293	38293	type	True	100.0	1677	1680	95	conclusive
Photobacterium damselae subsp. damselae	strain=CIP 102761	GCA_000176795.1	85581	38293	type	True	99.992	1644	1680	95	conclusive
Photobacterium damselae	strain=ATCC 33539	GCA_003026815.1	38293	38293	type	True	99.9452	1558	1680	95	conclusive
Vibrio inusitatus	strain=LMG 23434	GCA_024346935.1	413402	413402	type	True	80.4522	148	1680	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.3324	189	1680	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.0106	177	1680	95	below_threshold
Photobacterium leiognathi	strain=ATCC 25521	GCA_003026235.1	553611	553611	type	True	79.8654	447	1680	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	79.8041	464	1680	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	79.7791	169	1680	95	below_threshold
Photobacterium leiognathi	strain=ATCC 25521	GCA_000950415.1	553611	553611	type	True	79.7078	458	1680	95	below_threshold
Photobacterium lucens	strain=CAIM 1937	GCA_009873615.1	2562949	2562949	type	True	79.5513	436	1680	95	below_threshold
Photobacterium angustum	strain=ATCC 25915	GCA_003026365.1	661	661	type	True	79.424	417	1680	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.3559	175	1680	95	below_threshold
Photobacterium angustum	strain=ATCC 25915	GCA_000950005.1	661	661	type	True	79.2436	414	1680	95	below_threshold
Photobacterium marinum	strain=AK15	GCA_000331515.1	1056511	1056511	type	True	79.0357	288	1680	95	below_threshold
Vibrio inusitatus	strain=NBRC 102082	GCA_006538525.1	413402	413402	type	True	78.739	130	1680	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	78.7341	404	1680	95	below_threshold
Photobacterium indicum	strain=ATCC 19614	GCA_003026215.1	81447	81447	type	True	78.5661	358	1680	95	below_threshold
Vibrio variabilis	strain=CAIM 1454	GCA_003263785.1	990271	990271	type	True	78.4618	167	1680	95	below_threshold
Photobacterium frigidiphilum	strain=JCM 12947	GCA_003025615.1	264736	264736	type	True	78.4612	349	1680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:38,991] [INFO] DFAST Taxonomy check result was written to GCF_900454585.1_49950_G01_genomic.fna/tc_result.tsv
[2024-01-24 13:22:38,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:38,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:38,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c1b387a-0995-413a-95a2-647032843841/dqc_reference/checkm_data
[2024-01-24 13:22:38,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:39,041] [INFO] Task started: CheckM
[2024-01-24 13:22:39,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900454585.1_49950_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900454585.1_49950_G01_genomic.fna/checkm_input GCF_900454585.1_49950_G01_genomic.fna/checkm_result
[2024-01-24 13:23:18,585] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:18,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:18,610] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:18,611] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:18,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900454585.1_49950_G01_genomic.fna/markers.fasta)
[2024-01-24 13:23:18,612] [INFO] Task started: Blastn
[2024-01-24 13:23:18,612] [INFO] Running command: blastn -query GCF_900454585.1_49950_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c1b387a-0995-413a-95a2-647032843841/dqc_reference/reference_markers_gtdb.fasta -out GCF_900454585.1_49950_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:19,662] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:19,665] [INFO] Selected 19 target genomes.
[2024-01-24 13:23:19,665] [INFO] Target genome list was writen to GCF_900454585.1_49950_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:19,697] [INFO] Task started: fastANI
[2024-01-24 13:23:19,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg433ce11b-3956-4551-9ed7-2709ddde416c/GCF_900454585.1_49950_G01_genomic.fna.gz --refList GCF_900454585.1_49950_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900454585.1_49950_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:36,864] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:36,884] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:36,884] [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_003026815.1	s__Photobacterium damselae	99.9452	1558	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.68	96.10	0.89	0.75	54	conclusive
GCF_000940995.1	s__Photobacterium gaetbulicola	80.0025	260	1680	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	79.7137	456	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.11	96.59	0.91	0.88	15	-
GCF_003026105.1	s__Photobacterium sp003026105	79.6673	406	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.17	99.06	0.96	0.95	8	-
GCF_009873615.1	s__Photobacterium lucens	79.5817	433	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.83	97.58	0.96	0.94	5	-
GCF_003026365.1	s__Photobacterium angustum	79.4105	417	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.76	95.45	0.92	0.87	27	-
GCF_000153325.1	s__Photobacterium sp000153325	79.3156	394	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026495.1	s__Photobacterium sanctipauli	79.2452	290	1680	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	79.2065	270	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_900233005.1	s__Vibrio tapetis	79.1417	174	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650345.1	s__Photobacterium jeanii	79.0957	355	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000331515.1	s__Photobacterium marinum	79.0725	285	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_001077885.1	s__Photobacterium swingsii	79.0137	347	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000695685.1	s__Vibrio fortis	78.8435	170	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	-
GCF_003026355.1	s__Photobacterium kishitanii	78.7484	411	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.67	97.61	0.95	0.91	24	-
GCF_006538525.1	s__Vibrio inusitatus	78.7078	129	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026285.1	s__Photobacterium profundum	78.6593	345	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000775715.1	s__Vibrio tubiashii_A	78.6517	160	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026215.1	s__Photobacterium indicum	78.5639	355	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:36,886] [INFO] GTDB search result was written to GCF_900454585.1_49950_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:36,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:36,891] [INFO] DFAST_QC result json was written to GCF_900454585.1_49950_G01_genomic.fna/dqc_result.json
[2024-01-24 13:23:36,891] [INFO] DFAST_QC completed!
[2024-01-24 13:23:36,891] [INFO] Total running time: 0h1m36s