[2024-01-24 12:47:18,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:18,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:18,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg4230cb93-6b5a-422b-b613-b3503305ea13/dqc_reference
[2024-01-24 12:47:19,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:19,819] [INFO] Task started: Prodigal
[2024-01-24 12:47:19,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg18596236-828e-421e-a627-b3240fdcda3c/GCF_008933155.1_ASM893315v1_genomic.fna.gz | prodigal -d GCF_008933155.1_ASM893315v1_genomic.fna/cds.fna -a GCF_008933155.1_ASM893315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:28,419] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:28,420] [INFO] Task started: HMMsearch
[2024-01-24 12:47:28,420] [INFO] Running command: hmmsearch --tblout GCF_008933155.1_ASM893315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4230cb93-6b5a-422b-b613-b3503305ea13/dqc_reference/reference_markers.hmm GCF_008933155.1_ASM893315v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:28,658] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:28,659] [INFO] Found 6/6 markers.
[2024-01-24 12:47:28,691] [INFO] Query marker FASTA was written to GCF_008933155.1_ASM893315v1_genomic.fna/markers.fasta
[2024-01-24 12:47:28,691] [INFO] Task started: Blastn
[2024-01-24 12:47:28,692] [INFO] Running command: blastn -query GCF_008933155.1_ASM893315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4230cb93-6b5a-422b-b613-b3503305ea13/dqc_reference/reference_markers.fasta -out GCF_008933155.1_ASM893315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:29,538] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:29,541] [INFO] Selected 13 target genomes.
[2024-01-24 12:47:29,541] [INFO] Target genome list was writen to GCF_008933155.1_ASM893315v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:29,547] [INFO] Task started: fastANI
[2024-01-24 12:47:29,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg18596236-828e-421e-a627-b3240fdcda3c/GCF_008933155.1_ASM893315v1_genomic.fna.gz --refList GCF_008933155.1_ASM893315v1_genomic.fna/target_genomes.txt --output GCF_008933155.1_ASM893315v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:40,781] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:40,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4230cb93-6b5a-422b-b613-b3503305ea13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:40,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4230cb93-6b5a-422b-b613-b3503305ea13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:40,794] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:40,794] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:40,794] [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
Aliivibrio finisterrensis	strain=LMG 23869	GCA_008933155.1	511998	511998	suspected-type	True	100.0	1256	1260	95	conclusive
Aliivibrio sifiae	strain=NBRC 105001	GCA_002954715.1	566293	566293	type	True	85.4116	973	1260	95	below_threshold
Aliivibrio fischeri	strain=ATCC 7744	GCA_016464335.1	668	668	suspected-type	True	84.5903	850	1260	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	84.5181	876	1260	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	79.4979	277	1260	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.1517	279	1260	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.0494	278	1260	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.393	194	1260	95	below_threshold
Vibrio gangliei	strain=SZDIS-1	GCA_002934045.1	2077090	2077090	type	True	78.2235	184	1260	95	below_threshold
Vibrio penaeicida	strain=IFO 15640	GCA_019977755.1	104609	104609	type	True	78.1379	184	1260	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	78.1208	199	1260	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	78.1164	212	1260	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	77.952	206	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:40,796] [INFO] DFAST Taxonomy check result was written to GCF_008933155.1_ASM893315v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:40,798] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:40,798] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:40,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4230cb93-6b5a-422b-b613-b3503305ea13/dqc_reference/checkm_data
[2024-01-24 12:47:40,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:40,838] [INFO] Task started: CheckM
[2024-01-24 12:47:40,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008933155.1_ASM893315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008933155.1_ASM893315v1_genomic.fna/checkm_input GCF_008933155.1_ASM893315v1_genomic.fna/checkm_result
[2024-01-24 12:48:10,590] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:10,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:10,612] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:10,612] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:10,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008933155.1_ASM893315v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:10,612] [INFO] Task started: Blastn
[2024-01-24 12:48:10,613] [INFO] Running command: blastn -query GCF_008933155.1_ASM893315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4230cb93-6b5a-422b-b613-b3503305ea13/dqc_reference/reference_markers_gtdb.fasta -out GCF_008933155.1_ASM893315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:11,803] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:11,807] [INFO] Selected 9 target genomes.
[2024-01-24 12:48:11,807] [INFO] Target genome list was writen to GCF_008933155.1_ASM893315v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:11,826] [INFO] Task started: fastANI
[2024-01-24 12:48:11,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg18596236-828e-421e-a627-b3240fdcda3c/GCF_008933155.1_ASM893315v1_genomic.fna.gz --refList GCF_008933155.1_ASM893315v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008933155.1_ASM893315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:21,818] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:21,826] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:21,826] [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_008933155.1	s__Aliivibrio finisterrensis	100.0	1256	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	95.53	95.03	0.81	0.80	11	conclusive
GCF_900312675.1	s__Aliivibrio sp900312675	88.8915	1019	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000953695.1	s__Aliivibrio wodanis	86.5831	924	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954705.1	s__Aliivibrio sifiae_A	86.2409	938	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954715.1	s__Aliivibrio sifiae	85.4397	969	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	98.51	98.40	0.92	0.91	7	-
GCF_001690985.1	s__Aliivibrio sp001690985	85.2046	912	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	99.59	99.19	0.97	0.95	3	-
GCF_016464335.1	s__Aliivibrio fischeri	84.5935	850	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.1568	96.45	95.48	0.88	0.84	60	-
GCF_009727955.1	s__Aliivibrio fischeri_A	84.3731	889	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.1568	98.75	97.87	0.96	0.92	6	-
GCF_000196495.1	s__Aliivibrio salmonicida_A	83.1099	814	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	97.90	97.13	0.84	0.80	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:21,829] [INFO] GTDB search result was written to GCF_008933155.1_ASM893315v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:21,830] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:21,833] [INFO] DFAST_QC result json was written to GCF_008933155.1_ASM893315v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:21,833] [INFO] DFAST_QC completed!
[2024-01-24 12:48:21,833] [INFO] Total running time: 0h1m3s