[2024-01-24 15:10:40,219] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:40,223] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:40,224] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4fc268c-409b-4ad5-8e67-13eb46ca35ab/dqc_reference
[2024-01-24 15:10:41,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:41,577] [INFO] Task started: Prodigal
[2024-01-24 15:10:41,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d0cb788-ab80-4b92-b8b7-43113c9747b2/GCF_000696385.1_OP3Hv1_genomic.fna.gz | prodigal -d GCF_000696385.1_OP3Hv1_genomic.fna/cds.fna -a GCF_000696385.1_OP3Hv1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:52,977] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:52,978] [INFO] Task started: HMMsearch
[2024-01-24 15:10:52,978] [INFO] Running command: hmmsearch --tblout GCF_000696385.1_OP3Hv1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4fc268c-409b-4ad5-8e67-13eb46ca35ab/dqc_reference/reference_markers.hmm GCF_000696385.1_OP3Hv1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:53,281] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:53,282] [INFO] Found 6/6 markers.
[2024-01-24 15:10:53,329] [INFO] Query marker FASTA was written to GCF_000696385.1_OP3Hv1_genomic.fna/markers.fasta
[2024-01-24 15:10:53,329] [INFO] Task started: Blastn
[2024-01-24 15:10:53,329] [INFO] Running command: blastn -query GCF_000696385.1_OP3Hv1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4fc268c-409b-4ad5-8e67-13eb46ca35ab/dqc_reference/reference_markers.fasta -out GCF_000696385.1_OP3Hv1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:54,257] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:54,260] [INFO] Selected 10 target genomes.
[2024-01-24 15:10:54,260] [INFO] Target genome list was writen to GCF_000696385.1_OP3Hv1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:54,264] [INFO] Task started: fastANI
[2024-01-24 15:10:54,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d0cb788-ab80-4b92-b8b7-43113c9747b2/GCF_000696385.1_OP3Hv1_genomic.fna.gz --refList GCF_000696385.1_OP3Hv1_genomic.fna/target_genomes.txt --output GCF_000696385.1_OP3Hv1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:06,423] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:06,424] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4fc268c-409b-4ad5-8e67-13eb46ca35ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:06,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4fc268c-409b-4ad5-8e67-13eb46ca35ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:06,436] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:06,436] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:06,436] [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 metoecus	strain=OP3H	GCA_000696385.1	1481663	1481663	type	True	100.0	1280	1286	95	conclusive
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	88.9191	1057	1286	95	below_threshold
Vibrio cholerae	strain=ATCC 14035	GCA_000621645.1	666	666	type	True	88.361	1041	1286	95	below_threshold
Vibrio paracholerae	strain=EDC-792	GCA_017169525.1	650003	650003	type	True	88.0437	1007	1286	95	below_threshold
Vibrio mimicus	strain=CAIM 602	GCA_000338875.1	674	674	type	True	87.7743	1035	1286	95	below_threshold
Vibrio mimicus	strain=NCTC11435	GCA_900460385.1	674	674	type	True	87.7417	1041	1286	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	79.527	500	1286	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	79.1138	310	1286	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	78.5208	279	1286	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	78.0174	283	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:06,438] [INFO] DFAST Taxonomy check result was written to GCF_000696385.1_OP3Hv1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:06,439] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:06,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:06,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4fc268c-409b-4ad5-8e67-13eb46ca35ab/dqc_reference/checkm_data
[2024-01-24 15:11:06,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:06,492] [INFO] Task started: CheckM
[2024-01-24 15:11:06,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000696385.1_OP3Hv1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000696385.1_OP3Hv1_genomic.fna/checkm_input GCF_000696385.1_OP3Hv1_genomic.fna/checkm_result
[2024-01-24 15:11:43,927] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:43,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:43,949] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:43,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:43,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000696385.1_OP3Hv1_genomic.fna/markers.fasta)
[2024-01-24 15:11:43,951] [INFO] Task started: Blastn
[2024-01-24 15:11:43,951] [INFO] Running command: blastn -query GCF_000696385.1_OP3Hv1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4fc268c-409b-4ad5-8e67-13eb46ca35ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_000696385.1_OP3Hv1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:45,236] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:45,240] [INFO] Selected 5 target genomes.
[2024-01-24 15:11:45,240] [INFO] Target genome list was writen to GCF_000696385.1_OP3Hv1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:45,245] [INFO] Task started: fastANI
[2024-01-24 15:11:45,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d0cb788-ab80-4b92-b8b7-43113c9747b2/GCF_000696385.1_OP3Hv1_genomic.fna.gz --refList GCF_000696385.1_OP3Hv1_genomic.fna/target_genomes_gtdb.txt --output GCF_000696385.1_OP3Hv1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:51,158] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:51,164] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:51,164] [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_000696385.1	s__Vibrio metoecus	100.0	1280	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.79	97.58	0.93	0.89	26	conclusive
GCF_009665255.1	s__Vibrio metoecus_B	94.257	1178	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.11	98.11	0.94	0.94	2	-
GCF_019048845.1	s__Vibrio sp000176715	88.4888	1028	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.20	96.20	0.92	0.92	2	-
GCF_001471585.2	s__Vibrio cholerae	88.4146	1028	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.72	95.09	0.90	0.82	1544	-
GCF_000338875.1	s__Vibrio mimicus	87.7691	1035	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.81	0.94	0.91	26	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:51,170] [INFO] GTDB search result was written to GCF_000696385.1_OP3Hv1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:51,170] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:51,175] [INFO] DFAST_QC result json was written to GCF_000696385.1_OP3Hv1_genomic.fna/dqc_result.json
[2024-01-24 15:11:51,175] [INFO] DFAST_QC completed!
[2024-01-24 15:11:51,176] [INFO] Total running time: 0h1m11s