[2024-01-25 20:12:50,418] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:50,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:50,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg7731ce1b-15aa-4071-9c32-7d7361f77bb9/dqc_reference
[2024-01-25 20:12:51,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:51,521] [INFO] Task started: Prodigal
[2024-01-25 20:12:51,522] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5f514f5-dd54-49fc-89df-56118732411f/GCF_003026455.1_ASM302645v1_genomic.fna.gz | prodigal -d GCF_003026455.1_ASM302645v1_genomic.fna/cds.fna -a GCF_003026455.1_ASM302645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:06,167] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:06,167] [INFO] Task started: HMMsearch
[2024-01-25 20:13:06,167] [INFO] Running command: hmmsearch --tblout GCF_003026455.1_ASM302645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7731ce1b-15aa-4071-9c32-7d7361f77bb9/dqc_reference/reference_markers.hmm GCF_003026455.1_ASM302645v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:06,541] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:06,543] [INFO] Found 6/6 markers.
[2024-01-25 20:13:06,596] [INFO] Query marker FASTA was written to GCF_003026455.1_ASM302645v1_genomic.fna/markers.fasta
[2024-01-25 20:13:06,596] [INFO] Task started: Blastn
[2024-01-25 20:13:06,596] [INFO] Running command: blastn -query GCF_003026455.1_ASM302645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7731ce1b-15aa-4071-9c32-7d7361f77bb9/dqc_reference/reference_markers.fasta -out GCF_003026455.1_ASM302645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:07,384] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:07,387] [INFO] Selected 14 target genomes.
[2024-01-25 20:13:07,387] [INFO] Target genome list was writen to GCF_003026455.1_ASM302645v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:07,400] [INFO] Task started: fastANI
[2024-01-25 20:13:07,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5f514f5-dd54-49fc-89df-56118732411f/GCF_003026455.1_ASM302645v1_genomic.fna.gz --refList GCF_003026455.1_ASM302645v1_genomic.fna/target_genomes.txt --output GCF_003026455.1_ASM302645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:22,435] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:22,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7731ce1b-15aa-4071-9c32-7d7361f77bb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:22,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7731ce1b-15aa-4071-9c32-7d7361f77bb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:22,444] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:13:22,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:22,444] [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 rosenbergii	strain=DSM 19138	GCA_003026455.1	294936	294936	type	True	100.0	2082	2085	95	conclusive
Photobacterium gaetbulicola	strain=DSM 26887	GCA_003025515.1	1295392	1295392	type	True	84.7691	1314	2085	95	below_threshold
Photobacterium gaetbulicola	strain=Gung47	GCA_000940995.1	1295392	1295392	type	True	84.7628	1332	2085	95	below_threshold
Photobacterium lutimaris	strain=JCM 13586	GCA_003025555.1	388278	388278	type	True	83.4345	1225	2085	95	below_threshold
Photobacterium sanctipauli	strain=A-394	GCA_000730475.1	1342794	1342794	type	True	81.0546	584	2085	95	below_threshold
Photobacterium sanctipauli	strain=DSM 100436	GCA_003026495.1	1342794	1342794	type	True	80.7821	818	2085	95	below_threshold
Photobacterium aquae	strain=CGMCC 1.12159	GCA_001029445.1	1195763	1195763	type	True	80.4302	561	2085	95	below_threshold
Photobacterium proteolyticum	strain=13-12	GCA_001939735.1	1903952	1903952	type	True	79.9964	610	2085	95	below_threshold
Photobacterium jeanii	strain=R-40508	GCA_001650345.1	858640	858640	type	True	79.7403	453	2085	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.3734	435	2085	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	78.5246	219	2085	95	below_threshold
Vibrio spartinae	strain=CECT 9026	GCA_024347135.1	1918945	1918945	type	True	77.3652	83	2085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:22,445] [INFO] DFAST Taxonomy check result was written to GCF_003026455.1_ASM302645v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:22,446] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:22,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:22,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7731ce1b-15aa-4071-9c32-7d7361f77bb9/dqc_reference/checkm_data
[2024-01-25 20:13:22,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:22,508] [INFO] Task started: CheckM
[2024-01-25 20:13:22,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003026455.1_ASM302645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003026455.1_ASM302645v1_genomic.fna/checkm_input GCF_003026455.1_ASM302645v1_genomic.fna/checkm_result
[2024-01-25 20:14:07,711] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:07,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:07,768] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:07,768] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:07,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003026455.1_ASM302645v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:07,770] [INFO] Task started: Blastn
[2024-01-25 20:14:07,770] [INFO] Running command: blastn -query GCF_003026455.1_ASM302645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7731ce1b-15aa-4071-9c32-7d7361f77bb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003026455.1_ASM302645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:08,990] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:08,993] [INFO] Selected 9 target genomes.
[2024-01-25 20:14:08,993] [INFO] Target genome list was writen to GCF_003026455.1_ASM302645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:09,004] [INFO] Task started: fastANI
[2024-01-25 20:14:09,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5f514f5-dd54-49fc-89df-56118732411f/GCF_003026455.1_ASM302645v1_genomic.fna.gz --refList GCF_003026455.1_ASM302645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003026455.1_ASM302645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:19,582] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:19,588] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:19,588] [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_003026455.1	s__Photobacterium rosenbergii	100.0	2082	2085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	conclusive
GCF_000940995.1	s__Photobacterium gaetbulicola	84.7677	1331	2085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.90	95.81	0.93	0.87	3	-
GCF_003025555.1	s__Photobacterium lutimaris	83.4252	1227	2085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003026495.1	s__Photobacterium sanctipauli	80.7811	819	2085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001029445.1	s__Photobacterium aquae	80.4302	561	2085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001029435.1	s__Photobacterium aphoticum	80.3725	626	2085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.09	97.29	0.97	0.93	4	-
GCF_000331515.1	s__Photobacterium marinum	80.0757	528	2085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_001939735.1	s__Photobacterium proteolyticum	80.0008	609	2085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650345.1	s__Photobacterium jeanii	79.7382	451	2085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:19,590] [INFO] GTDB search result was written to GCF_003026455.1_ASM302645v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:19,591] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:19,594] [INFO] DFAST_QC result json was written to GCF_003026455.1_ASM302645v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:19,594] [INFO] DFAST_QC completed!
[2024-01-25 20:14:19,594] [INFO] Total running time: 0h1m29s