[2024-01-24 11:35:22,917] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:22,920] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:22,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg11a10091-01bb-43fa-9cc5-b8cd47d40df8/dqc_reference
[2024-01-24 11:35:26,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,242] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg63c98a40-1d69-41ce-b24d-5e0d1e9085a9/GCF_014652075.1_ASM1465207v1_genomic.fna.gz | prodigal -d GCF_014652075.1_ASM1465207v1_genomic.fna/cds.fna -a GCF_014652075.1_ASM1465207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:41,973] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:41,973] [INFO] Task started: HMMsearch
[2024-01-24 11:35:41,973] [INFO] Running command: hmmsearch --tblout GCF_014652075.1_ASM1465207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11a10091-01bb-43fa-9cc5-b8cd47d40df8/dqc_reference/reference_markers.hmm GCF_014652075.1_ASM1465207v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:42,333] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:42,334] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg63c98a40-1d69-41ce-b24d-5e0d1e9085a9/GCF_014652075.1_ASM1465207v1_genomic.fna.gz]
[2024-01-24 11:35:42,374] [INFO] Query marker FASTA was written to GCF_014652075.1_ASM1465207v1_genomic.fna/markers.fasta
[2024-01-24 11:35:42,375] [INFO] Task started: Blastn
[2024-01-24 11:35:42,375] [INFO] Running command: blastn -query GCF_014652075.1_ASM1465207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11a10091-01bb-43fa-9cc5-b8cd47d40df8/dqc_reference/reference_markers.fasta -out GCF_014652075.1_ASM1465207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:43,254] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:43,258] [INFO] Selected 15 target genomes.
[2024-01-24 11:35:43,258] [INFO] Target genome list was writen to GCF_014652075.1_ASM1465207v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:43,288] [INFO] Task started: fastANI
[2024-01-24 11:35:43,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c98a40-1d69-41ce-b24d-5e0d1e9085a9/GCF_014652075.1_ASM1465207v1_genomic.fna.gz --refList GCF_014652075.1_ASM1465207v1_genomic.fna/target_genomes.txt --output GCF_014652075.1_ASM1465207v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:57,626] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:57,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11a10091-01bb-43fa-9cc5-b8cd47d40df8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:57,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11a10091-01bb-43fa-9cc5-b8cd47d40df8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:57,640] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:35:57,641] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:57,641] [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 aphoticum	strain=KCTC 23057	GCA_014652075.1	754436	754436	type	True	100.0	1727	1733	95	conclusive
Photobacterium aphoticum	strain=DSM 25995	GCA_001029435.1	754436	754436	type	True	99.9824	1700	1733	95	conclusive
Photobacterium aphoticum	strain=DSM 25995	GCA_003025575.1	754436	754436	type	True	99.9141	1608	1733	95	conclusive
Photobacterium aquae	strain=CGMCC 1.12159	GCA_001029445.1	1195763	1195763	type	True	80.4402	601	1733	95	below_threshold
Photobacterium gaetbulicola	strain=DSM 26887	GCA_003025515.1	1295392	1295392	type	True	80.3969	631	1733	95	below_threshold
Photobacterium gaetbulicola	strain=Gung47	GCA_000940995.1	1295392	1295392	type	True	80.364	643	1733	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	80.0696	615	1733	95	below_threshold
Photobacterium ganghwense	strain=DSM 22954	GCA_001029455.1	320778	320778	type	True	79.9482	613	1733	95	below_threshold
Photobacterium marinum	strain=AK15	GCA_000331515.1	1056511	1056511	type	True	79.73	481	1733	95	below_threshold
Photobacterium jeanii	strain=R-40508	GCA_001650345.1	858640	858640	type	True	79.564	463	1733	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.2812	414	1733	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	78.9567	403	1733	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.741	190	1733	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.6793	187	1733	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	78.4125	317	1733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:57,643] [INFO] DFAST Taxonomy check result was written to GCF_014652075.1_ASM1465207v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:57,643] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:57,644] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:57,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11a10091-01bb-43fa-9cc5-b8cd47d40df8/dqc_reference/checkm_data
[2024-01-24 11:35:57,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:57,700] [INFO] Task started: CheckM
[2024-01-24 11:35:57,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652075.1_ASM1465207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652075.1_ASM1465207v1_genomic.fna/checkm_input GCF_014652075.1_ASM1465207v1_genomic.fna/checkm_result
[2024-01-24 11:36:47,271] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:47,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:47,293] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:47,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:47,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652075.1_ASM1465207v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:47,295] [INFO] Task started: Blastn
[2024-01-24 11:36:47,295] [INFO] Running command: blastn -query GCF_014652075.1_ASM1465207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11a10091-01bb-43fa-9cc5-b8cd47d40df8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652075.1_ASM1465207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:48,539] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:48,543] [INFO] Selected 11 target genomes.
[2024-01-24 11:36:48,543] [INFO] Target genome list was writen to GCF_014652075.1_ASM1465207v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:48,552] [INFO] Task started: fastANI
[2024-01-24 11:36:48,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c98a40-1d69-41ce-b24d-5e0d1e9085a9/GCF_014652075.1_ASM1465207v1_genomic.fna.gz --refList GCF_014652075.1_ASM1465207v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652075.1_ASM1465207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:00,713] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:00,732] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:00,732] [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_001029435.1	s__Photobacterium aphoticum	99.9824	1700	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.09	97.29	0.97	0.93	4	conclusive
GCF_003026455.1	s__Photobacterium rosenbergii	80.5362	597	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_001029445.1	s__Photobacterium aquae	80.4354	602	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000940995.1	s__Photobacterium gaetbulicola	80.3499	645	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.90	95.81	0.93	0.87	3	-
GCF_003026495.1	s__Photobacterium sanctipauli	80.3034	597	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025555.1	s__Photobacterium lutimaris	80.2376	607	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003025595.1	s__Photobacterium ganghwense	80.0641	616	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.50	98.82	0.97	0.96	4	-
GCF_009910675.1	s__Photobacterium alginatilyticum	79.9689	507	1733	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	79.8061	513	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331515.1	s__Photobacterium marinum	79.7408	480	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_001650345.1	s__Photobacterium jeanii	79.564	463	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:00,734] [INFO] GTDB search result was written to GCF_014652075.1_ASM1465207v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:00,734] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:00,738] [INFO] DFAST_QC result json was written to GCF_014652075.1_ASM1465207v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:00,738] [INFO] DFAST_QC completed!
[2024-01-24 11:37:00,738] [INFO] Total running time: 0h1m38s