[2024-01-24 11:13:49,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:49,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:49,602] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb906bc1-6800-46b2-bd60-74d0dbb5fce9/dqc_reference
[2024-01-24 11:13:50,821] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:50,821] [INFO] Task started: Prodigal
[2024-01-24 11:13:50,822] [INFO] Running command: gunzip -c /var/lib/cwl/stg659cb367-3dfb-4fe1-99a7-096d629ae98f/GCF_003025975.1_ASM302597v1_genomic.fna.gz | prodigal -d GCF_003025975.1_ASM302597v1_genomic.fna/cds.fna -a GCF_003025975.1_ASM302597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:14:00,552] [INFO] Task succeeded: Prodigal
[2024-01-24 11:14:00,553] [INFO] Task started: HMMsearch
[2024-01-24 11:14:00,553] [INFO] Running command: hmmsearch --tblout GCF_003025975.1_ASM302597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb906bc1-6800-46b2-bd60-74d0dbb5fce9/dqc_reference/reference_markers.hmm GCF_003025975.1_ASM302597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:14:00,864] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:14:00,866] [INFO] Found 6/6 markers.
[2024-01-24 11:14:00,906] [INFO] Query marker FASTA was written to GCF_003025975.1_ASM302597v1_genomic.fna/markers.fasta
[2024-01-24 11:14:00,906] [INFO] Task started: Blastn
[2024-01-24 11:14:00,906] [INFO] Running command: blastn -query GCF_003025975.1_ASM302597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb906bc1-6800-46b2-bd60-74d0dbb5fce9/dqc_reference/reference_markers.fasta -out GCF_003025975.1_ASM302597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:01,703] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:01,707] [INFO] Selected 15 target genomes.
[2024-01-24 11:14:01,708] [INFO] Target genome list was writen to GCF_003025975.1_ASM302597v1_genomic.fna/target_genomes.txt
[2024-01-24 11:14:01,714] [INFO] Task started: fastANI
[2024-01-24 11:14:01,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg659cb367-3dfb-4fe1-99a7-096d629ae98f/GCF_003025975.1_ASM302597v1_genomic.fna.gz --refList GCF_003025975.1_ASM302597v1_genomic.fna/target_genomes.txt --output GCF_003025975.1_ASM302597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:16,380] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:16,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb906bc1-6800-46b2-bd60-74d0dbb5fce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:16,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb906bc1-6800-46b2-bd60-74d0dbb5fce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:16,404] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:14:16,405] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:14:16,405] [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 kishitanii	strain=pjapo.1.1	GCA_003025975.1	318456	318456	type	True	100.0	1552	1555	95	conclusive
Photobacterium kishitanii	strain=ATCC:BAA-1194	GCA_003026355.1	318456	318456	type	True	99.9937	1541	1555	95	conclusive
Photobacterium kishitanii	strain=ATCC BAA-1194	GCA_000950095.1	318456	318456	type	True	99.9773	1519	1555	95	conclusive
Photobacterium phosphoreum	strain=JCM 21184	GCA_002954725.1	659	659	type	True	86.7738	1223	1555	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	86.7498	1213	1555	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_003026275.1	659	659	type	True	86.7436	1244	1555	95	below_threshold
Photobacterium aquimaris	strain=DSM 23343	GCA_003025415.1	512643	512643	suspected-type	True	86.501	1170	1555	95	below_threshold
Photobacterium malacitanum	strain=CECT 9190	GCA_900185615.1	2204294	2204294	type	True	86.1724	1176	1555	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	85.457	1092	1555	95	below_threshold
Photobacterium carnosum	strain=TMW 2.2021	GCA_002849605.1	2023717	2023717	type	True	85.4247	1050	1555	95	below_threshold
Photobacterium iliopiscarium	strain=ATCC 51760	GCA_000950265.1	56192	56192	type	True	85.3092	1104	1555	95	below_threshold
Photobacterium piscicola	strain=type strain: NCCB 100098	GCA_900166965.1	1378299	1378299	type	True	85.2446	1152	1555	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.2574	326	1555	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	78.2866	109	1555	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	77.7863	150	1555	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:16,406] [INFO] DFAST Taxonomy check result was written to GCF_003025975.1_ASM302597v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:16,407] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:16,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:16,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb906bc1-6800-46b2-bd60-74d0dbb5fce9/dqc_reference/checkm_data
[2024-01-24 11:14:16,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:16,450] [INFO] Task started: CheckM
[2024-01-24 11:14:16,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003025975.1_ASM302597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003025975.1_ASM302597v1_genomic.fna/checkm_input GCF_003025975.1_ASM302597v1_genomic.fna/checkm_result
[2024-01-24 11:14:50,465] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:50,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:50,487] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:50,487] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:50,488] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003025975.1_ASM302597v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:50,488] [INFO] Task started: Blastn
[2024-01-24 11:14:50,489] [INFO] Running command: blastn -query GCF_003025975.1_ASM302597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb906bc1-6800-46b2-bd60-74d0dbb5fce9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003025975.1_ASM302597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:51,675] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:51,679] [INFO] Selected 8 target genomes.
[2024-01-24 11:14:51,679] [INFO] Target genome list was writen to GCF_003025975.1_ASM302597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:51,702] [INFO] Task started: fastANI
[2024-01-24 11:14:51,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg659cb367-3dfb-4fe1-99a7-096d629ae98f/GCF_003025975.1_ASM302597v1_genomic.fna.gz --refList GCF_003025975.1_ASM302597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003025975.1_ASM302597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:01,056] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:01,067] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:01,067] [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_003026355.1	s__Photobacterium kishitanii	99.9937	1541	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.67	97.61	0.95	0.91	24	conclusive
GCF_002954725.1	s__Photobacterium phosphoreum	86.7701	1224	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.41	96.65	0.93	0.88	23	-
GCF_002954455.1	s__Photobacterium aquimaris	86.4573	1185	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.51	95.34	0.95	0.87	6	-
GCF_900185615.1	s__Photobacterium malacitanum	86.1643	1177	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.08	95.06	0.91	0.91	6	-
GCF_002849605.1	s__Photobacterium carnosum	85.4181	1051	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.77	98.77	0.93	0.93	2	-
GCF_003026395.1	s__Photobacterium iliopiscarium	85.3764	1127	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.31	98.95	0.95	0.91	7	-
GCF_900166975.1	s__Photobacterium toruni	85.368	1078	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166965.1	s__Photobacterium piscicola	85.2446	1152	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.92	98.92	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:01,069] [INFO] GTDB search result was written to GCF_003025975.1_ASM302597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:01,069] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:01,073] [INFO] DFAST_QC result json was written to GCF_003025975.1_ASM302597v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:01,073] [INFO] DFAST_QC completed!
[2024-01-24 11:15:01,073] [INFO] Total running time: 0h1m11s