[2024-01-25 20:14:20,723] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:20,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:20,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fc1fb39-1826-45bc-a7c1-24b953a3ac80/dqc_reference
[2024-01-25 20:14:21,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:21,829] [INFO] Task started: Prodigal
[2024-01-25 20:14:21,829] [INFO] Running command: gunzip -c /var/lib/cwl/stg512b1647-74f4-465a-9a3a-4715adeb5be4/GCF_000950095.1_CFSAN029432_01.0_genomic.fna.gz | prodigal -d GCF_000950095.1_CFSAN029432_01.0_genomic.fna/cds.fna -a GCF_000950095.1_CFSAN029432_01.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:29,988] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:29,988] [INFO] Task started: HMMsearch
[2024-01-25 20:14:29,988] [INFO] Running command: hmmsearch --tblout GCF_000950095.1_CFSAN029432_01.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fc1fb39-1826-45bc-a7c1-24b953a3ac80/dqc_reference/reference_markers.hmm GCF_000950095.1_CFSAN029432_01.0_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:30,224] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:30,225] [INFO] Found 6/6 markers.
[2024-01-25 20:14:30,264] [INFO] Query marker FASTA was written to GCF_000950095.1_CFSAN029432_01.0_genomic.fna/markers.fasta
[2024-01-25 20:14:30,264] [INFO] Task started: Blastn
[2024-01-25 20:14:30,265] [INFO] Running command: blastn -query GCF_000950095.1_CFSAN029432_01.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fc1fb39-1826-45bc-a7c1-24b953a3ac80/dqc_reference/reference_markers.fasta -out GCF_000950095.1_CFSAN029432_01.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:31,000] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:31,003] [INFO] Selected 15 target genomes.
[2024-01-25 20:14:31,003] [INFO] Target genome list was writen to GCF_000950095.1_CFSAN029432_01.0_genomic.fna/target_genomes.txt
[2024-01-25 20:14:31,008] [INFO] Task started: fastANI
[2024-01-25 20:14:31,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg512b1647-74f4-465a-9a3a-4715adeb5be4/GCF_000950095.1_CFSAN029432_01.0_genomic.fna.gz --refList GCF_000950095.1_CFSAN029432_01.0_genomic.fna/target_genomes.txt --output GCF_000950095.1_CFSAN029432_01.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:46,340] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:46,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fc1fb39-1826-45bc-a7c1-24b953a3ac80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:46,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fc1fb39-1826-45bc-a7c1-24b953a3ac80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:46,351] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:14:46,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:46,351] [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=ATCC BAA-1194	GCA_000950095.1	318456	318456	type	True	100.0	1529	1533	95	conclusive
Photobacterium kishitanii	strain=pjapo.1.1	GCA_003025975.1	318456	318456	type	True	99.9853	1520	1533	95	conclusive
Photobacterium kishitanii	strain=ATCC:BAA-1194	GCA_003026355.1	318456	318456	type	True	99.9817	1521	1533	95	conclusive
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	86.7066	1214	1533	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_003026275.1	659	659	type	True	86.702	1221	1533	95	below_threshold
Photobacterium phosphoreum	strain=JCM 21184	GCA_002954725.1	659	659	type	True	86.6206	1244	1533	95	below_threshold
Photobacterium aquimaris	strain=DSM 23343	GCA_003025415.1	512643	512643	suspected-type	True	86.5126	1162	1533	95	below_threshold
Photobacterium malacitanum	strain=CECT 9190	GCA_900185615.1	2204294	2204294	type	True	86.1074	1169	1533	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	85.435	1087	1533	95	below_threshold
Photobacterium carnosum	strain=TMW 2.2021	GCA_002849605.1	2023717	2023717	type	True	85.3747	1065	1533	95	below_threshold
Photobacterium iliopiscarium	strain=ATCC 51760	GCA_000950265.1	56192	56192	type	True	85.3001	1092	1533	95	below_threshold
Photobacterium piscicola	strain=type strain: NCCB 100098	GCA_900166965.1	1378299	1378299	type	True	85.2892	1137	1533	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.23	336	1533	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	78.1096	114	1533	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	77.5866	157	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:46,352] [INFO] DFAST Taxonomy check result was written to GCF_000950095.1_CFSAN029432_01.0_genomic.fna/tc_result.tsv
[2024-01-25 20:14:46,353] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:46,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:46,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fc1fb39-1826-45bc-a7c1-24b953a3ac80/dqc_reference/checkm_data
[2024-01-25 20:14:46,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:46,399] [INFO] Task started: CheckM
[2024-01-25 20:14:46,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000950095.1_CFSAN029432_01.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000950095.1_CFSAN029432_01.0_genomic.fna/checkm_input GCF_000950095.1_CFSAN029432_01.0_genomic.fna/checkm_result
[2024-01-25 20:15:14,334] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:14,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:14,353] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:14,353] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:14,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000950095.1_CFSAN029432_01.0_genomic.fna/markers.fasta)
[2024-01-25 20:15:14,353] [INFO] Task started: Blastn
[2024-01-25 20:15:14,353] [INFO] Running command: blastn -query GCF_000950095.1_CFSAN029432_01.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fc1fb39-1826-45bc-a7c1-24b953a3ac80/dqc_reference/reference_markers_gtdb.fasta -out GCF_000950095.1_CFSAN029432_01.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:15,478] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:15,480] [INFO] Selected 8 target genomes.
[2024-01-25 20:15:15,480] [INFO] Target genome list was writen to GCF_000950095.1_CFSAN029432_01.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:15,484] [INFO] Task started: fastANI
[2024-01-25 20:15:15,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg512b1647-74f4-465a-9a3a-4715adeb5be4/GCF_000950095.1_CFSAN029432_01.0_genomic.fna.gz --refList GCF_000950095.1_CFSAN029432_01.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000950095.1_CFSAN029432_01.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:24,125] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:24,132] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:24,132] [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	99.9817	1521	1533	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	86.6304	1243	1533	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	86.4858	1182	1533	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	86.0809	1172	1533	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	85.3825	1064	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.77	98.77	0.93	0.93	2	-
GCF_900166975.1	s__Photobacterium toruni	85.363	1082	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026395.1	s__Photobacterium iliopiscarium	85.3197	1116	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.31	98.95	0.95	0.91	7	-
GCF_900166965.1	s__Photobacterium piscicola	85.2946	1137	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.92	98.92	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:24,133] [INFO] GTDB search result was written to GCF_000950095.1_CFSAN029432_01.0_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:24,134] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:24,137] [INFO] DFAST_QC result json was written to GCF_000950095.1_CFSAN029432_01.0_genomic.fna/dqc_result.json
[2024-01-25 20:15:24,137] [INFO] DFAST_QC completed!
[2024-01-25 20:15:24,137] [INFO] Total running time: 0h1m3s