[2024-01-24 12:40:35,400] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:35,401] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:35,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg19747d59-7576-43ae-ae40-1625755437b6/dqc_reference
[2024-01-24 12:40:36,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:36,677] [INFO] Task started: Prodigal
[2024-01-24 12:40:36,677] [INFO] Running command: gunzip -c /var/lib/cwl/stg17023563-1601-408a-82f3-089d2948320c/GCF_001077885.1_CAIM1393T.ver1_genomic.fna.gz | prodigal -d GCF_001077885.1_CAIM1393T.ver1_genomic.fna/cds.fna -a GCF_001077885.1_CAIM1393T.ver1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:49,343] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:49,343] [INFO] Task started: HMMsearch
[2024-01-24 12:40:49,343] [INFO] Running command: hmmsearch --tblout GCF_001077885.1_CAIM1393T.ver1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19747d59-7576-43ae-ae40-1625755437b6/dqc_reference/reference_markers.hmm GCF_001077885.1_CAIM1393T.ver1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:49,657] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:49,658] [INFO] Found 6/6 markers.
[2024-01-24 12:40:49,704] [INFO] Query marker FASTA was written to GCF_001077885.1_CAIM1393T.ver1_genomic.fna/markers.fasta
[2024-01-24 12:40:49,705] [INFO] Task started: Blastn
[2024-01-24 12:40:49,705] [INFO] Running command: blastn -query GCF_001077885.1_CAIM1393T.ver1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19747d59-7576-43ae-ae40-1625755437b6/dqc_reference/reference_markers.fasta -out GCF_001077885.1_CAIM1393T.ver1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:50,509] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:50,533] [INFO] Selected 8 target genomes.
[2024-01-24 12:40:50,534] [INFO] Target genome list was writen to GCF_001077885.1_CAIM1393T.ver1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:50,540] [INFO] Task started: fastANI
[2024-01-24 12:40:50,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg17023563-1601-408a-82f3-089d2948320c/GCF_001077885.1_CAIM1393T.ver1_genomic.fna.gz --refList GCF_001077885.1_CAIM1393T.ver1_genomic.fna/target_genomes.txt --output GCF_001077885.1_CAIM1393T.ver1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:59,216] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:59,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19747d59-7576-43ae-ae40-1625755437b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:59,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19747d59-7576-43ae-ae40-1625755437b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:59,228] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:40:59,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:59,228] [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 swingsii	strain=CAIM 1393	GCA_001077885.1	680026	680026	type	True	100.0	1797	1800	95	conclusive
Photobacterium swingsii	strain=DSM 24669	GCA_003026435.1	680026	680026	type	True	99.9772	1800	1800	95	conclusive
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	99.9768	1799	1800	95	conclusive
Photobacterium sanguinicancri	strain=CAIM 1827	GCA_002265265.1	875932	875932	type	True	86.3839	1317	1800	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	86.3215	1486	1800	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	78.294	224	1800	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	77.8545	125	1800	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	77.5715	160	1800	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:59,230] [INFO] DFAST Taxonomy check result was written to GCF_001077885.1_CAIM1393T.ver1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:59,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:59,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:59,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19747d59-7576-43ae-ae40-1625755437b6/dqc_reference/checkm_data
[2024-01-24 12:40:59,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:59,288] [INFO] Task started: CheckM
[2024-01-24 12:40:59,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001077885.1_CAIM1393T.ver1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001077885.1_CAIM1393T.ver1_genomic.fna/checkm_input GCF_001077885.1_CAIM1393T.ver1_genomic.fna/checkm_result
[2024-01-24 12:41:40,765] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:40,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:40,787] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:40,787] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:40,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001077885.1_CAIM1393T.ver1_genomic.fna/markers.fasta)
[2024-01-24 12:41:40,788] [INFO] Task started: Blastn
[2024-01-24 12:41:40,789] [INFO] Running command: blastn -query GCF_001077885.1_CAIM1393T.ver1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19747d59-7576-43ae-ae40-1625755437b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001077885.1_CAIM1393T.ver1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:41,919] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:41,923] [INFO] Selected 14 target genomes.
[2024-01-24 12:41:41,924] [INFO] Target genome list was writen to GCF_001077885.1_CAIM1393T.ver1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:41,933] [INFO] Task started: fastANI
[2024-01-24 12:41:41,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg17023563-1601-408a-82f3-089d2948320c/GCF_001077885.1_CAIM1393T.ver1_genomic.fna.gz --refList GCF_001077885.1_CAIM1393T.ver1_genomic.fna/target_genomes_gtdb.txt --output GCF_001077885.1_CAIM1393T.ver1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:55,489] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:55,513] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:55,514] [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_001077885.1	s__Photobacterium swingsii	100.0	1797	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_002265265.1	s__Photobacterium sanguinicancri	86.4057	1314	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.87	97.87	0.90	0.90	2	-
GCF_001650345.1	s__Photobacterium jeanii	81.8174	926	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000950415.1	s__Photobacterium leiognathi	79.6703	377	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.11	96.59	0.91	0.88	15	-
GCF_004104355.1	s__Photobacterium chitinilyticum	79.6386	428	1800	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	79.6329	407	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026105.1	s__Photobacterium sp003026105	79.3993	341	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.17	99.06	0.96	0.95	8	-
GCF_001939735.1	s__Photobacterium proteolyticum	79.3483	420	1800	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	79.3405	399	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_000153325.1	s__Photobacterium sp000153325	79.2355	338	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185615.1	s__Photobacterium malacitanum	79.2177	321	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.08	95.06	0.91	0.91	6	-
GCF_003026215.1	s__Photobacterium indicum	79.185	512	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954455.1	s__Photobacterium aquimaris	79.1348	326	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.51	95.34	0.95	0.87	6	-
GCF_003026285.1	s__Photobacterium profundum	79.0359	513	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.97	99.97	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:55,515] [INFO] GTDB search result was written to GCF_001077885.1_CAIM1393T.ver1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:55,516] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:55,519] [INFO] DFAST_QC result json was written to GCF_001077885.1_CAIM1393T.ver1_genomic.fna/dqc_result.json
[2024-01-24 12:41:55,519] [INFO] DFAST_QC completed!
[2024-01-24 12:41:55,519] [INFO] Total running time: 0h1m20s