[2024-01-25 17:43:05,502] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:05,504] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:05,504] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa4cd72c-5bf1-4b62-90d7-12455994a652/dqc_reference
[2024-01-25 17:43:06,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:06,660] [INFO] Task started: Prodigal
[2024-01-25 17:43:06,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg36cbec27-782c-4436-ba9f-5e0ab32437c6/GCF_001029445.1_ASM102944v1_genomic.fna.gz | prodigal -d GCF_001029445.1_ASM102944v1_genomic.fna/cds.fna -a GCF_001029445.1_ASM102944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:18,928] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:18,929] [INFO] Task started: HMMsearch
[2024-01-25 17:43:18,929] [INFO] Running command: hmmsearch --tblout GCF_001029445.1_ASM102944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa4cd72c-5bf1-4b62-90d7-12455994a652/dqc_reference/reference_markers.hmm GCF_001029445.1_ASM102944v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:19,219] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:19,220] [INFO] Found 6/6 markers.
[2024-01-25 17:43:19,268] [INFO] Query marker FASTA was written to GCF_001029445.1_ASM102944v1_genomic.fna/markers.fasta
[2024-01-25 17:43:19,268] [INFO] Task started: Blastn
[2024-01-25 17:43:19,268] [INFO] Running command: blastn -query GCF_001029445.1_ASM102944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa4cd72c-5bf1-4b62-90d7-12455994a652/dqc_reference/reference_markers.fasta -out GCF_001029445.1_ASM102944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:20,053] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:20,055] [INFO] Selected 18 target genomes.
[2024-01-25 17:43:20,056] [INFO] Target genome list was writen to GCF_001029445.1_ASM102944v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:20,069] [INFO] Task started: fastANI
[2024-01-25 17:43:20,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg36cbec27-782c-4436-ba9f-5e0ab32437c6/GCF_001029445.1_ASM102944v1_genomic.fna.gz --refList GCF_001029445.1_ASM102944v1_genomic.fna/target_genomes.txt --output GCF_001029445.1_ASM102944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:38,272] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:38,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa4cd72c-5bf1-4b62-90d7-12455994a652/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:38,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa4cd72c-5bf1-4b62-90d7-12455994a652/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:38,283] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:43:38,283] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:38,284] [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 aquae	strain=CGMCC 1.12159	GCA_001029445.1	1195763	1195763	type	True	100.0	1646	1651	95	conclusive
Photobacterium aphoticum	strain=DSM 25995	GCA_003025575.1	754436	754436	type	True	80.6139	563	1651	95	below_threshold
Photobacterium aphoticum	strain=DSM 25995	GCA_001029435.1	754436	754436	type	True	80.5321	594	1651	95	below_threshold
Photobacterium aphoticum	strain=KCTC 23057	GCA_014652075.1	754436	754436	type	True	80.4693	594	1651	95	below_threshold
Photobacterium gaetbulicola	strain=DSM 26887	GCA_003025515.1	1295392	1295392	type	True	80.3455	580	1651	95	below_threshold
Photobacterium rosenbergii	strain=DSM 19138	GCA_003026455.1	294936	294936	type	True	80.3241	549	1651	95	below_threshold
Photobacterium gaetbulicola	strain=Gung47	GCA_000940995.1	1295392	1295392	type	True	80.3162	586	1651	95	below_threshold
Photobacterium sanctipauli	strain=A-394	GCA_000730475.1	1342794	1342794	type	True	80.1858	393	1651	95	below_threshold
Photobacterium sanctipauli	strain=DSM 100436	GCA_003026495.1	1342794	1342794	type	True	79.9794	536	1651	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	79.8283	525	1651	95	below_threshold
Photobacterium ganghwense	strain=DSM 22954	GCA_001029455.1	320778	320778	type	True	79.7816	526	1651	95	below_threshold
Photobacterium alginatilyticum	strain=P03D4	GCA_009910675.1	1775171	1775171	type	True	79.5906	514	1651	95	below_threshold
Photobacterium marinum	strain=AK15	GCA_000331515.1	1056511	1056511	type	True	79.5062	482	1651	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.0621	332	1651	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	78.7837	319	1651	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	78.0408	154	1651	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	77.9492	281	1651	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	77.8337	162	1651	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:38,285] [INFO] DFAST Taxonomy check result was written to GCF_001029445.1_ASM102944v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:38,286] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:38,286] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:38,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa4cd72c-5bf1-4b62-90d7-12455994a652/dqc_reference/checkm_data
[2024-01-25 17:43:38,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:38,338] [INFO] Task started: CheckM
[2024-01-25 17:43:38,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001029445.1_ASM102944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001029445.1_ASM102944v1_genomic.fna/checkm_input GCF_001029445.1_ASM102944v1_genomic.fna/checkm_result
[2024-01-25 17:44:17,211] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:17,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:17,234] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:17,234] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:17,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001029445.1_ASM102944v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:17,235] [INFO] Task started: Blastn
[2024-01-25 17:44:17,235] [INFO] Running command: blastn -query GCF_001029445.1_ASM102944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa4cd72c-5bf1-4b62-90d7-12455994a652/dqc_reference/reference_markers_gtdb.fasta -out GCF_001029445.1_ASM102944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:18,495] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:18,498] [INFO] Selected 10 target genomes.
[2024-01-25 17:44:18,498] [INFO] Target genome list was writen to GCF_001029445.1_ASM102944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:18,530] [INFO] Task started: fastANI
[2024-01-25 17:44:18,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg36cbec27-782c-4436-ba9f-5e0ab32437c6/GCF_001029445.1_ASM102944v1_genomic.fna.gz --refList GCF_001029445.1_ASM102944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001029445.1_ASM102944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:29,626] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:29,633] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:29,633] [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_001029445.1	s__Photobacterium aquae	100.0	1646	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001029435.1	s__Photobacterium aphoticum	80.5267	594	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.09	97.29	0.97	0.93	4	-
GCF_003026455.1	s__Photobacterium rosenbergii	80.3269	548	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_000940995.1	s__Photobacterium gaetbulicola	80.3163	586	1651	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	79.963	538	1651	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	79.9019	573	1651	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	79.8396	523	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.50	98.82	0.97	0.96	4	-
GCF_001939735.1	s__Photobacterium proteolyticum	79.6958	517	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009910675.1	s__Photobacterium alginatilyticum	79.5906	514	1651	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	79.4971	483	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:29,635] [INFO] GTDB search result was written to GCF_001029445.1_ASM102944v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:29,635] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:29,638] [INFO] DFAST_QC result json was written to GCF_001029445.1_ASM102944v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:29,639] [INFO] DFAST_QC completed!
[2024-01-25 17:44:29,639] [INFO] Total running time: 0h1m24s