[2024-01-25 17:47:35,619] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:35,623] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:35,623] [INFO] DQC Reference Directory: /var/lib/cwl/stgf243001c-d2c7-4334-88b5-1935a9bbe45a/dqc_reference
[2024-01-25 17:47:36,757] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:36,757] [INFO] Task started: Prodigal
[2024-01-25 17:47:36,758] [INFO] Running command: gunzip -c /var/lib/cwl/stg90d639f2-8153-47d7-b234-225f0dccb27e/GCF_024346715.1_ASM2434671v1_genomic.fna.gz | prodigal -d GCF_024346715.1_ASM2434671v1_genomic.fna/cds.fna -a GCF_024346715.1_ASM2434671v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:48,409] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:48,410] [INFO] Task started: HMMsearch
[2024-01-25 17:47:48,410] [INFO] Running command: hmmsearch --tblout GCF_024346715.1_ASM2434671v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf243001c-d2c7-4334-88b5-1935a9bbe45a/dqc_reference/reference_markers.hmm GCF_024346715.1_ASM2434671v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:48,704] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:48,705] [INFO] Found 6/6 markers.
[2024-01-25 17:47:48,747] [INFO] Query marker FASTA was written to GCF_024346715.1_ASM2434671v1_genomic.fna/markers.fasta
[2024-01-25 17:47:48,748] [INFO] Task started: Blastn
[2024-01-25 17:47:48,748] [INFO] Running command: blastn -query GCF_024346715.1_ASM2434671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf243001c-d2c7-4334-88b5-1935a9bbe45a/dqc_reference/reference_markers.fasta -out GCF_024346715.1_ASM2434671v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:49,501] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:49,504] [INFO] Selected 8 target genomes.
[2024-01-25 17:47:49,504] [INFO] Target genome list was writen to GCF_024346715.1_ASM2434671v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:49,510] [INFO] Task started: fastANI
[2024-01-25 17:47:49,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg90d639f2-8153-47d7-b234-225f0dccb27e/GCF_024346715.1_ASM2434671v1_genomic.fna.gz --refList GCF_024346715.1_ASM2434671v1_genomic.fna/target_genomes.txt --output GCF_024346715.1_ASM2434671v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:59,615] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:59,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf243001c-d2c7-4334-88b5-1935a9bbe45a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:59,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf243001c-d2c7-4334-88b5-1935a9bbe45a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:59,622] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:47:59,622] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:59,622] [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=CECT 7576	GCA_024346715.1	680026	680026	type	True	100.0	1879	1882	95	conclusive
Photobacterium swingsii	strain=DSM 24669	GCA_003026435.1	680026	680026	type	True	99.9859	1824	1882	95	conclusive
Photobacterium swingsii	strain=CAIM 1393	GCA_001077885.1	680026	680026	type	True	99.9516	1797	1882	95	conclusive
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	86.5961	1539	1882	95	below_threshold
Photobacterium sanguinicancri	strain=CAIM 1827	GCA_002265265.1	875932	875932	type	True	86.3761	1347	1882	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	80.1256	151	1882	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	79.3304	262	1882	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	79.0408	183	1882	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:59,623] [INFO] DFAST Taxonomy check result was written to GCF_024346715.1_ASM2434671v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:59,624] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:59,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:59,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf243001c-d2c7-4334-88b5-1935a9bbe45a/dqc_reference/checkm_data
[2024-01-25 17:47:59,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:59,678] [INFO] Task started: CheckM
[2024-01-25 17:47:59,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024346715.1_ASM2434671v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024346715.1_ASM2434671v1_genomic.fna/checkm_input GCF_024346715.1_ASM2434671v1_genomic.fna/checkm_result
[2024-01-25 17:48:38,282] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:38,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:38,309] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:38,309] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:38,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024346715.1_ASM2434671v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:38,310] [INFO] Task started: Blastn
[2024-01-25 17:48:38,310] [INFO] Running command: blastn -query GCF_024346715.1_ASM2434671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf243001c-d2c7-4334-88b5-1935a9bbe45a/dqc_reference/reference_markers_gtdb.fasta -out GCF_024346715.1_ASM2434671v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:39,494] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:39,497] [INFO] Selected 15 target genomes.
[2024-01-25 17:48:39,497] [INFO] Target genome list was writen to GCF_024346715.1_ASM2434671v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:39,517] [INFO] Task started: fastANI
[2024-01-25 17:48:39,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg90d639f2-8153-47d7-b234-225f0dccb27e/GCF_024346715.1_ASM2434671v1_genomic.fna.gz --refList GCF_024346715.1_ASM2434671v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024346715.1_ASM2434671v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:55,803] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:55,813] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:48:55,813] [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	99.9516	1797	1882	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	86.3585	1350	1882	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	81.732	948	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004104355.1	s__Photobacterium chitinilyticum	79.8535	440	1882	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	79.7939	429	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000950415.1	s__Photobacterium leiognathi	79.6617	391	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.11	96.59	0.91	0.88	15	-
GCF_000153325.1	s__Photobacterium sp000153325	79.5354	369	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001939735.1	s__Photobacterium proteolyticum	79.4519	452	1882	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	79.4295	416	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_003026105.1	s__Photobacterium sp003026105	79.4205	362	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.17	99.06	0.96	0.95	8	-
GCF_003026215.1	s__Photobacterium indicum	79.3884	533	1882	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	79.3649	338	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.08	95.06	0.91	0.91	6	-
GCF_000331515.1	s__Photobacterium marinum	79.2729	395	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_003026285.1	s__Photobacterium profundum	79.2518	544	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_002954455.1	s__Photobacterium aquimaris	79.2284	340	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.51	95.34	0.95	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:55,815] [INFO] GTDB search result was written to GCF_024346715.1_ASM2434671v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:55,815] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:55,818] [INFO] DFAST_QC result json was written to GCF_024346715.1_ASM2434671v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:55,818] [INFO] DFAST_QC completed!
[2024-01-25 17:48:55,818] [INFO] Total running time: 0h1m20s