[2024-01-24 13:12:52,574] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:52,576] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:52,576] [INFO] DQC Reference Directory: /var/lib/cwl/stge5106a83-c603-4ad0-9bff-f112e47f27dd/dqc_reference
[2024-01-24 13:12:53,953] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:53,954] [INFO] Task started: Prodigal
[2024-01-24 13:12:53,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf26e6ec-7659-4ae3-b2ea-3d7ccdd743e1/GCF_030398735.1_ASM3039873v1_genomic.fna.gz | prodigal -d GCF_030398735.1_ASM3039873v1_genomic.fna/cds.fna -a GCF_030398735.1_ASM3039873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:07,713] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:07,714] [INFO] Task started: HMMsearch
[2024-01-24 13:13:07,714] [INFO] Running command: hmmsearch --tblout GCF_030398735.1_ASM3039873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5106a83-c603-4ad0-9bff-f112e47f27dd/dqc_reference/reference_markers.hmm GCF_030398735.1_ASM3039873v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:08,109] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:08,110] [INFO] Found 6/6 markers.
[2024-01-24 13:13:08,186] [INFO] Query marker FASTA was written to GCF_030398735.1_ASM3039873v1_genomic.fna/markers.fasta
[2024-01-24 13:13:08,187] [INFO] Task started: Blastn
[2024-01-24 13:13:08,187] [INFO] Running command: blastn -query GCF_030398735.1_ASM3039873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5106a83-c603-4ad0-9bff-f112e47f27dd/dqc_reference/reference_markers.fasta -out GCF_030398735.1_ASM3039873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:09,046] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:09,049] [INFO] Selected 10 target genomes.
[2024-01-24 13:13:09,050] [INFO] Target genome list was writen to GCF_030398735.1_ASM3039873v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:09,054] [INFO] Task started: fastANI
[2024-01-24 13:13:09,054] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf26e6ec-7659-4ae3-b2ea-3d7ccdd743e1/GCF_030398735.1_ASM3039873v1_genomic.fna.gz --refList GCF_030398735.1_ASM3039873v1_genomic.fna/target_genomes.txt --output GCF_030398735.1_ASM3039873v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:20,019] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:20,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5106a83-c603-4ad0-9bff-f112e47f27dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:20,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5106a83-c603-4ad0-9bff-f112e47f27dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:20,029] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:13:20,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:20,030] [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
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001998785.1	670	670	type	True	98.3951	1540	1617	95	conclusive
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	98.3951	1536	1617	95	conclusive
Vibrio parahaemolyticus		GCA_001558495.2	670	670	type	True	98.3885	1547	1617	95	conclusive
Vibrio parahaemolyticus	strain=NBRC 12711	GCA_000813305.1	670	670	type	True	98.3756	1529	1617	95	conclusive
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	98.3567	1543	1617	95	conclusive
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	83.2427	947	1617	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.5384	382	1617	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.5266	390	1617	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.9555	473	1617	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.2512	370	1617	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:20,031] [INFO] DFAST Taxonomy check result was written to GCF_030398735.1_ASM3039873v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:20,032] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:20,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:20,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5106a83-c603-4ad0-9bff-f112e47f27dd/dqc_reference/checkm_data
[2024-01-24 13:13:20,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:20,083] [INFO] Task started: CheckM
[2024-01-24 13:13:20,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030398735.1_ASM3039873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030398735.1_ASM3039873v1_genomic.fna/checkm_input GCF_030398735.1_ASM3039873v1_genomic.fna/checkm_result
[2024-01-24 13:14:03,720] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:03,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,745] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:03,746] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:03,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030398735.1_ASM3039873v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:03,746] [INFO] Task started: Blastn
[2024-01-24 13:14:03,746] [INFO] Running command: blastn -query GCF_030398735.1_ASM3039873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5106a83-c603-4ad0-9bff-f112e47f27dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_030398735.1_ASM3039873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:04,975] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:04,980] [INFO] Selected 12 target genomes.
[2024-01-24 13:14:04,980] [INFO] Target genome list was writen to GCF_030398735.1_ASM3039873v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:04,990] [INFO] Task started: fastANI
[2024-01-24 13:14:04,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf26e6ec-7659-4ae3-b2ea-3d7ccdd743e1/GCF_030398735.1_ASM3039873v1_genomic.fna.gz --refList GCF_030398735.1_ASM3039873v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030398735.1_ASM3039873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:18,057] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:18,074] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:18,074] [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_900460535.1	s__Vibrio parahaemolyticus	98.3567	1543	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	conclusive
GCA_001048675.1	s__Vibrio diabolicus	86.8895	1296	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_000354175.2	s__Vibrio alginolyticus	86.2561	1210	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_000817815.1	s__Vibrio owensii	83.8191	1053	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_002163755.1	s__Vibrio campbellii	83.6707	999	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_001591145.1	s__Vibrio harveyi	83.5901	1071	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_000400365.1	s__Vibrio jasicida	83.4902	1029	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_002741985.1	s__Vibrio rotiferianus	83.4059	967	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_000417905.1	s__Vibrio natriegens	83.2502	924	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	-
GCA_018223135.1	s__Vibrio sp018223135	82.9999	846	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222805.1	s__Vibrio sp018222805	82.8772	847	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905175385.1	s__Vibrio sp903986855	82.5644	877	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.95	0.95	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:18,076] [INFO] GTDB search result was written to GCF_030398735.1_ASM3039873v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:18,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:18,080] [INFO] DFAST_QC result json was written to GCF_030398735.1_ASM3039873v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:18,080] [INFO] DFAST_QC completed!
[2024-01-24 13:14:18,080] [INFO] Total running time: 0h1m26s