[2024-01-24 15:26:47,453] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:47,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:47,455] [INFO] DQC Reference Directory: /var/lib/cwl/stgc024135f-73b6-48d0-bc99-0ed72f1dd2d5/dqc_reference
[2024-01-24 15:26:48,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:48,657] [INFO] Task started: Prodigal
[2024-01-24 15:26:48,657] [INFO] Running command: gunzip -c /var/lib/cwl/stgcad41b12-d704-43af-a0ee-d361e3d66dd3/GCF_000950415.1_CFSAN029437_01.0_genomic.fna.gz | prodigal -d GCF_000950415.1_CFSAN029437_01.0_genomic.fna/cds.fna -a GCF_000950415.1_CFSAN029437_01.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:58,124] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:58,125] [INFO] Task started: HMMsearch
[2024-01-24 15:26:58,125] [INFO] Running command: hmmsearch --tblout GCF_000950415.1_CFSAN029437_01.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc024135f-73b6-48d0-bc99-0ed72f1dd2d5/dqc_reference/reference_markers.hmm GCF_000950415.1_CFSAN029437_01.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:58,409] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:58,411] [INFO] Found 6/6 markers.
[2024-01-24 15:26:58,455] [INFO] Query marker FASTA was written to GCF_000950415.1_CFSAN029437_01.0_genomic.fna/markers.fasta
[2024-01-24 15:26:58,456] [INFO] Task started: Blastn
[2024-01-24 15:26:58,456] [INFO] Running command: blastn -query GCF_000950415.1_CFSAN029437_01.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgc024135f-73b6-48d0-bc99-0ed72f1dd2d5/dqc_reference/reference_markers.fasta -out GCF_000950415.1_CFSAN029437_01.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:59,281] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:59,285] [INFO] Selected 11 target genomes.
[2024-01-24 15:26:59,286] [INFO] Target genome list was writen to GCF_000950415.1_CFSAN029437_01.0_genomic.fna/target_genomes.txt
[2024-01-24 15:26:59,293] [INFO] Task started: fastANI
[2024-01-24 15:26:59,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad41b12-d704-43af-a0ee-d361e3d66dd3/GCF_000950415.1_CFSAN029437_01.0_genomic.fna.gz --refList GCF_000950415.1_CFSAN029437_01.0_genomic.fna/target_genomes.txt --output GCF_000950415.1_CFSAN029437_01.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:10,527] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:10,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc024135f-73b6-48d0-bc99-0ed72f1dd2d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:10,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc024135f-73b6-48d0-bc99-0ed72f1dd2d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:10,543] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:10,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:10,544] [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 leiognathi	strain=ATCC 25521	GCA_000950415.1	553611	553611	type	True	100.0	1476	1478	95	conclusive
Photobacterium leiognathi	strain=ATCC 25521	GCA_003026235.1	553611	553611	type	True	99.9776	1462	1478	95	conclusive
Photobacterium lucens	strain=CAIM 1937	GCA_009873615.1	2562949	2562949	type	True	93.1253	1115	1478	95	below_threshold
Photobacterium angustum	strain=ATCC 25915	GCA_003026365.1	661	661	type	True	84.7128	1100	1478	95	below_threshold
Photobacterium angustum	strain=ATCC 25915	GCA_000950005.1	661	661	type	True	84.7074	1082	1478	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	80.5831	549	1478	95	below_threshold
Photobacterium kishitanii	strain=ATCC:BAA-1194	GCA_003026355.1	318456	318456	type	True	80.2574	579	1478	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.5981	387	1478	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.2402	401	1478	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.5692	198	1478	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	78.3673	240	1478	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:10,550] [INFO] DFAST Taxonomy check result was written to GCF_000950415.1_CFSAN029437_01.0_genomic.fna/tc_result.tsv
[2024-01-24 15:27:10,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:10,550] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:10,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc024135f-73b6-48d0-bc99-0ed72f1dd2d5/dqc_reference/checkm_data
[2024-01-24 15:27:10,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:10,600] [INFO] Task started: CheckM
[2024-01-24 15:27:10,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000950415.1_CFSAN029437_01.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000950415.1_CFSAN029437_01.0_genomic.fna/checkm_input GCF_000950415.1_CFSAN029437_01.0_genomic.fna/checkm_result
[2024-01-24 15:27:44,859] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:44,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:44,880] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:44,880] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:44,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000950415.1_CFSAN029437_01.0_genomic.fna/markers.fasta)
[2024-01-24 15:27:44,881] [INFO] Task started: Blastn
[2024-01-24 15:27:44,882] [INFO] Running command: blastn -query GCF_000950415.1_CFSAN029437_01.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgc024135f-73b6-48d0-bc99-0ed72f1dd2d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000950415.1_CFSAN029437_01.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:46,141] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:46,145] [INFO] Selected 6 target genomes.
[2024-01-24 15:27:46,145] [INFO] Target genome list was writen to GCF_000950415.1_CFSAN029437_01.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:46,151] [INFO] Task started: fastANI
[2024-01-24 15:27:46,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad41b12-d704-43af-a0ee-d361e3d66dd3/GCF_000950415.1_CFSAN029437_01.0_genomic.fna.gz --refList GCF_000950415.1_CFSAN029437_01.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000950415.1_CFSAN029437_01.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:53,421] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:53,431] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:53,432] [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_000950415.1	s__Photobacterium leiognathi	100.0	1476	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.11	96.59	0.91	0.88	15	conclusive
GCF_009873615.1	s__Photobacterium lucens	93.1253	1115	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.83	97.58	0.96	0.94	5	-
GCF_003026105.1	s__Photobacterium sp003026105	84.8224	1078	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.17	99.06	0.96	0.95	8	-
GCF_003026365.1	s__Photobacterium angustum	84.7057	1101	1478	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	84.114	1050	1478	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	80.5096	600	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.51	95.34	0.95	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:53,434] [INFO] GTDB search result was written to GCF_000950415.1_CFSAN029437_01.0_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:53,434] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:53,437] [INFO] DFAST_QC result json was written to GCF_000950415.1_CFSAN029437_01.0_genomic.fna/dqc_result.json
[2024-01-24 15:27:53,437] [INFO] DFAST_QC completed!
[2024-01-24 15:27:53,438] [INFO] Total running time: 0h1m6s