[2024-01-24 13:01:52,883] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:52,885] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:52,885] [INFO] DQC Reference Directory: /var/lib/cwl/stg83f6a0b9-ac07-49f9-b07f-3186f15a2b7f/dqc_reference
[2024-01-24 13:01:54,160] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:54,161] [INFO] Task started: Prodigal
[2024-01-24 13:01:54,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg16d14dac-c2fd-4f42-b2d4-ab321cfc4990/GCF_001854765.1_ASM185476v1_genomic.fna.gz | prodigal -d GCF_001854765.1_ASM185476v1_genomic.fna/cds.fna -a GCF_001854765.1_ASM185476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:05,561] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:05,561] [INFO] Task started: HMMsearch
[2024-01-24 13:02:05,562] [INFO] Running command: hmmsearch --tblout GCF_001854765.1_ASM185476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83f6a0b9-ac07-49f9-b07f-3186f15a2b7f/dqc_reference/reference_markers.hmm GCF_001854765.1_ASM185476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:05,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:05,941] [INFO] Found 6/6 markers.
[2024-01-24 13:02:05,987] [INFO] Query marker FASTA was written to GCF_001854765.1_ASM185476v1_genomic.fna/markers.fasta
[2024-01-24 13:02:05,987] [INFO] Task started: Blastn
[2024-01-24 13:02:05,988] [INFO] Running command: blastn -query GCF_001854765.1_ASM185476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83f6a0b9-ac07-49f9-b07f-3186f15a2b7f/dqc_reference/reference_markers.fasta -out GCF_001854765.1_ASM185476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:06,811] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:06,814] [INFO] Selected 28 target genomes.
[2024-01-24 13:02:06,814] [INFO] Target genome list was writen to GCF_001854765.1_ASM185476v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:06,823] [INFO] Task started: fastANI
[2024-01-24 13:02:06,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg16d14dac-c2fd-4f42-b2d4-ab321cfc4990/GCF_001854765.1_ASM185476v1_genomic.fna.gz --refList GCF_001854765.1_ASM185476v1_genomic.fna/target_genomes.txt --output GCF_001854765.1_ASM185476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:28,844] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:28,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83f6a0b9-ac07-49f9-b07f-3186f15a2b7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:28,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83f6a0b9-ac07-49f9-b07f-3186f15a2b7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:28,865] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:28,865] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:28,865] [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 sonorensis	strain=CAIM 1076	GCA_001854765.1	1004316	1004316	type	True	100.0	1536	1539	95	conclusive
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	79.7591	359	1539	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	79.6886	365	1539	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	79.568	348	1539	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	79.5292	348	1539	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	79.4676	367	1539	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	79.4633	373	1539	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	79.4375	359	1539	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	79.4052	364	1539	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.3956	323	1539	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.3552	275	1539	95	below_threshold
Vibrio mexicanus	strain=CAIM 1540	GCA_001012815.1	1004326	1004326	type	True	79.3528	335	1539	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	79.3524	347	1539	95	below_threshold
Vibrio alginolyticus	strain=NCTC12160	GCA_900460285.1	663	663	type	True	79.3374	300	1539	95	below_threshold
Vibrio alginolyticus	strain=FDAARGOS_97	GCA_001471275.2	663	663	type	True	79.3352	304	1539	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	79.3345	309	1539	95	below_threshold
Vibrio variabilis	strain=CAIM 1454	GCA_003263785.1	990271	990271	type	True	79.3088	253	1539	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.2971	318	1539	95	below_threshold
Vibrio alginolyticus	strain=NBRC 15630	GCA_000467145.1	663	663	type	True	79.2587	293	1539	95	below_threshold
Vibrio maerlii	strain=G62	GCA_003415655.1	2231648	2231648	type	True	79.255	237	1539	95	below_threshold
Vibrio salilacus	strain=DSG-S6	GCA_002811245.1	1323749	1323749	type	True	79.224	310	1539	95	below_threshold
Vibrio xiamenensis	strain=CGMCC 1.10228	GCA_900100015.1	861298	861298	type	True	79.1269	284	1539	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.1063	308	1539	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.0532	292	1539	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	79.0278	260	1539	95	below_threshold
Vibrio penaeicida	strain=IFO 15640	GCA_019977755.1	104609	104609	type	True	78.8877	263	1539	95	below_threshold
Vibrio penaeicida	strain=CAIM 285	GCA_003970425.1	104609	104609	type	True	78.8206	249	1539	95	below_threshold
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	78.5215	260	1539	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:28,867] [INFO] DFAST Taxonomy check result was written to GCF_001854765.1_ASM185476v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:28,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:28,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:28,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83f6a0b9-ac07-49f9-b07f-3186f15a2b7f/dqc_reference/checkm_data
[2024-01-24 13:02:28,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:28,914] [INFO] Task started: CheckM
[2024-01-24 13:02:28,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001854765.1_ASM185476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001854765.1_ASM185476v1_genomic.fna/checkm_input GCF_001854765.1_ASM185476v1_genomic.fna/checkm_result
[2024-01-24 13:03:06,271] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:06,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:06,296] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:06,296] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:06,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001854765.1_ASM185476v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:06,297] [INFO] Task started: Blastn
[2024-01-24 13:03:06,297] [INFO] Running command: blastn -query GCF_001854765.1_ASM185476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83f6a0b9-ac07-49f9-b07f-3186f15a2b7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001854765.1_ASM185476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:07,543] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:07,553] [INFO] Selected 25 target genomes.
[2024-01-24 13:03:07,554] [INFO] Target genome list was writen to GCF_001854765.1_ASM185476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:07,567] [INFO] Task started: fastANI
[2024-01-24 13:03:07,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg16d14dac-c2fd-4f42-b2d4-ab321cfc4990/GCF_001854765.1_ASM185476v1_genomic.fna.gz --refList GCF_001854765.1_ASM185476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001854765.1_ASM185476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:27,694] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:27,720] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:27,720] [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_001854765.1	s__Vibrio sonorensis	100.0	1536	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013114545.1	s__Vibrio sp013114545	79.7387	365	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808535.1	s__Vibrio sinaloensis	79.696	383	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_000772105.1	s__Vibrio tubiashii	79.6886	365	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_010587385.1	s__Vibrio astriarenae	79.6214	240	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	96.60	0.82	0.82	2	-
GCF_009811315.1	s__Vibrio atypicus	79.5817	363	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_013113835.1	s__Vibrio sp013113835	79.5419	358	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006124995.1	s__Vibrio sp006124995	79.5412	338	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163755.1	s__Vibrio campbellii	79.539	314	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_001591105.1	s__Vibrio nereis	79.5292	348	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003970385.1	s__Vibrio aquaticus	79.4953	354	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176235.1	s__Vibrio orientalis	79.4771	372	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000189255.1	s__Vibrio brasiliensis	79.467	357	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176135.1	s__Vibrio coralliilyticus	79.4375	359	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_003350325.1	s__Vibrio rhodolitus	79.3524	347	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_013369335.1	s__Vibrio sp013369335	79.3516	343	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000817815.1	s__Vibrio owensii	79.3504	327	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCA_003263845.1	s__Vibrio aestivus	79.3453	306	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003263785.1	s__Vibrio variabilis	79.3092	252	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000354175.2	s__Vibrio alginolyticus	79.2736	307	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_001591145.1	s__Vibrio harveyi	79.2059	332	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_900100015.1	s__Vibrio xiamenensis	79.1106	285	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000755425.1	s__Vibrio maritimus_A	79.0791	269	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000755385.1	s__Vibrio maritimus_B	79.0479	260	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.88	95.88	0.85	0.85	2	-
GCF_003970425.1	s__Vibrio penaeicida	78.8212	249	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.14	96.14	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:27,722] [INFO] GTDB search result was written to GCF_001854765.1_ASM185476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:27,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:27,727] [INFO] DFAST_QC result json was written to GCF_001854765.1_ASM185476v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:27,727] [INFO] DFAST_QC completed!
[2024-01-24 13:03:27,727] [INFO] Total running time: 0h1m35s