[2024-01-24 11:51:50,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:50,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:50,245] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1c20b29-e28d-4d43-ad0b-b0bb67bb5560/dqc_reference
[2024-01-24 11:51:51,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,481] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d59f3ee-f366-49f0-b04e-1f95440399e0/GCF_003856525.1_ASM385652v1_genomic.fna.gz | prodigal -d GCF_003856525.1_ASM385652v1_genomic.fna/cds.fna -a GCF_003856525.1_ASM385652v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:01,690] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:01,690] [INFO] Task started: HMMsearch
[2024-01-24 11:52:01,691] [INFO] Running command: hmmsearch --tblout GCF_003856525.1_ASM385652v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1c20b29-e28d-4d43-ad0b-b0bb67bb5560/dqc_reference/reference_markers.hmm GCF_003856525.1_ASM385652v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:01,982] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:01,984] [INFO] Found 6/6 markers.
[2024-01-24 11:52:02,027] [INFO] Query marker FASTA was written to GCF_003856525.1_ASM385652v1_genomic.fna/markers.fasta
[2024-01-24 11:52:02,028] [INFO] Task started: Blastn
[2024-01-24 11:52:02,028] [INFO] Running command: blastn -query GCF_003856525.1_ASM385652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1c20b29-e28d-4d43-ad0b-b0bb67bb5560/dqc_reference/reference_markers.fasta -out GCF_003856525.1_ASM385652v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:02,863] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:02,866] [INFO] Selected 25 target genomes.
[2024-01-24 11:52:02,867] [INFO] Target genome list was writen to GCF_003856525.1_ASM385652v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:02,883] [INFO] Task started: fastANI
[2024-01-24 11:52:02,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d59f3ee-f366-49f0-b04e-1f95440399e0/GCF_003856525.1_ASM385652v1_genomic.fna.gz --refList GCF_003856525.1_ASM385652v1_genomic.fna/target_genomes.txt --output GCF_003856525.1_ASM385652v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:20,039] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:20,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1c20b29-e28d-4d43-ad0b-b0bb67bb5560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:20,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1c20b29-e28d-4d43-ad0b-b0bb67bb5560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:20,058] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:20,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:20,058] [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 viridaestus	strain=LJC006	GCA_003856525.1	2487322	2487322	type	True	100.0	1523	1525	95	conclusive
Vibrio salinus	strain=DNF-1	GCA_021272385.1	2899784	2899784	type	True	79.986	412	1525	95	below_threshold
Vibrio qinghaiensis	strain=Q67	GCA_002257545.1	2025808	2025808	type	True	79.0927	188	1525	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	79.0807	136	1525	95	below_threshold
Vibrio aestuarianus subsp. cardii	strain=12/122 3T3	GCA_011090275.1	2807650	28171	type	True	79.0489	198	1525	95	below_threshold
Vibrio alginolyticus	strain=NCTC12160	GCA_900460285.1	663	663	type	True	79.0118	184	1525	95	below_threshold
Vibrio alginolyticus	strain=ATCC 17749	GCA_000354175.2	663	663	type	True	78.9783	186	1525	95	below_threshold
Vibrio alginolyticus	strain=FDAARGOS_97	GCA_001471275.2	663	663	type	True	78.9422	184	1525	95	below_threshold
Vibrio anguillarum	strain=NCTC12159	GCA_900452855.1	55601	55601	type	True	78.9212	200	1525	95	below_threshold
Vibrio aestuarianus	strain=LMG 7909	GCA_012395185.1	28171	28171	type	True	78.9091	191	1525	95	below_threshold
Vibrio penaeicida	strain=IFO 15640	GCA_019977755.1	104609	104609	type	True	78.8651	150	1525	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.8534	180	1525	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.8359	176	1525	95	below_threshold
Vibrio penaeicida	strain=CAIM 285	GCA_003970425.1	104609	104609	type	True	78.833	137	1525	95	below_threshold
Vibrio alginolyticus	strain=NBRC 15630	GCA_000467145.1	663	663	type	True	78.7908	179	1525	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	78.7892	231	1525	95	below_threshold
Vibrio cholerae	strain=ATCC 14035	GCA_000621645.1	666	666	type	True	78.7091	159	1525	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	78.6932	182	1525	95	below_threshold
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	78.655	183	1525	95	below_threshold
Vibrio pectenicida	strain=LMG 19642	GCA_024347015.1	62763	62763	type	True	78.4501	144	1525	95	below_threshold
Vibrio sagamiensis	strain=NBRC 104589	GCA_000400425.1	512650	512650	type	True	78.4042	158	1525	95	below_threshold
Vibrio sagamiensis	strain=NBRC 104589	GCA_007990935.1	512650	512650	type	True	78.3666	156	1525	95	below_threshold
Vibrio palustris	strain=CECT 9027	GCA_024346995.1	1918946	1918946	type	True	78.302	180	1525	95	below_threshold
Aliivibrio finisterrensis	strain=LMG 23869	GCA_008933155.1	511998	511998	suspected-type	True	77.615	123	1525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:20,060] [INFO] DFAST Taxonomy check result was written to GCF_003856525.1_ASM385652v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:20,061] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:20,061] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:20,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1c20b29-e28d-4d43-ad0b-b0bb67bb5560/dqc_reference/checkm_data
[2024-01-24 11:52:20,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:20,106] [INFO] Task started: CheckM
[2024-01-24 11:52:20,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003856525.1_ASM385652v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003856525.1_ASM385652v1_genomic.fna/checkm_input GCF_003856525.1_ASM385652v1_genomic.fna/checkm_result
[2024-01-24 11:52:55,509] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:55,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.88%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:55,540] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:55,541] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:55,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003856525.1_ASM385652v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:55,542] [INFO] Task started: Blastn
[2024-01-24 11:52:55,542] [INFO] Running command: blastn -query GCF_003856525.1_ASM385652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1c20b29-e28d-4d43-ad0b-b0bb67bb5560/dqc_reference/reference_markers_gtdb.fasta -out GCF_003856525.1_ASM385652v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:56,730] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:56,733] [INFO] Selected 26 target genomes.
[2024-01-24 11:52:56,733] [INFO] Target genome list was writen to GCF_003856525.1_ASM385652v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:56,773] [INFO] Task started: fastANI
[2024-01-24 11:52:56,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d59f3ee-f366-49f0-b04e-1f95440399e0/GCF_003856525.1_ASM385652v1_genomic.fna.gz --refList GCF_003856525.1_ASM385652v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003856525.1_ASM385652v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:16,099] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:16,118] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:16,119] [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_003856525.1	s__Vibrio viridaestus	100.0	1523	1525	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_003605645.1	s__Vibrio sinensis	79.1588	166	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000257205.1	s__Vibrio ordalii	79.1375	166	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.90	98.90	0.96	0.96	2	-
GCF_000354175.2	s__Vibrio alginolyticus	78.9768	185	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_002933855.1	s__Vibrio penaeicida_A	78.9696	148	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900088415.1	s__Vibrio mediterranei	78.9515	166	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.1582	98.19	97.23	0.91	0.86	13	-
GCF_003544875.1	s__Vibrio alfacsensis	78.9488	178	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.49	96.49	0.89	0.89	2	-
GCF_012395185.1	s__Vibrio aestuarianus	78.9091	191	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.70	96.75	0.86	0.80	14	-
GCF_900460245.1	s__Vibrio fluvialis	78.8415	217	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_009938205.1	s__Vibrio panuliri	78.8352	176	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_015686695.1	s__Vibrio nitrifigilis	78.8224	230	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.79	98.79	0.95	0.95	2	-
GCF_001547935.1	s__Vibrio tritonius	78.8175	220	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278125.1	s__Vibrio sp015278125	78.8129	180	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970425.1	s__Vibrio penaeicida	78.8101	137	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.14	96.14	0.85	0.85	2	-
GCF_001471585.2	s__Vibrio cholerae	78.7513	162	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.72	95.09	0.90	0.82	1544	-
GCF_009938165.1	s__Vibrio taketomensis	78.7098	168	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_003970385.1	s__Vibrio aquaticus	78.6773	181	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641465.1	s__Vibrio agarilyticus	78.6695	134	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938225.1	s__Vibrio ponticus	78.655	183	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	-
GCF_001989995.2	s__Vibrio anguillarum	78.6273	192	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.39	98.01	0.89	0.80	121	-
GCF_001274785.1	s__Vibrio hepatarius	78.5392	199	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_000176135.1	s__Vibrio coralliilyticus	78.5066	189	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_014050145.1	s__Vibrio marinisediminis	78.4265	172	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990935.1	s__Vibrio sagamiensis	78.3666	156	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.95	99.91	0.97	0.96	3	-
GCF_002563795.1	s__Vibrio sp002563795	78.3618	187	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008933155.1	s__Aliivibrio finisterrensis	77.6252	124	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	95.53	95.03	0.81	0.80	11	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:16,121] [INFO] GTDB search result was written to GCF_003856525.1_ASM385652v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:16,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:16,126] [INFO] DFAST_QC result json was written to GCF_003856525.1_ASM385652v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:16,126] [INFO] DFAST_QC completed!
[2024-01-24 11:53:16,127] [INFO] Total running time: 0h1m26s