[2024-01-24 14:19:18,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:18,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:18,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg54ee0859-d1e7-496c-bf57-1f57b5c8bb47/dqc_reference
[2024-01-24 14:19:20,114] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:20,115] [INFO] Task started: Prodigal
[2024-01-24 14:19:20,115] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4866c62-d435-4009-86c7-fe43817698f9/GCF_003263785.1_ASM326378v1_genomic.fna.gz | prodigal -d GCF_003263785.1_ASM326378v1_genomic.fna/cds.fna -a GCF_003263785.1_ASM326378v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:33,540] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:33,540] [INFO] Task started: HMMsearch
[2024-01-24 14:19:33,540] [INFO] Running command: hmmsearch --tblout GCF_003263785.1_ASM326378v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54ee0859-d1e7-496c-bf57-1f57b5c8bb47/dqc_reference/reference_markers.hmm GCF_003263785.1_ASM326378v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:33,905] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:33,907] [INFO] Found 6/6 markers.
[2024-01-24 14:19:33,952] [INFO] Query marker FASTA was written to GCF_003263785.1_ASM326378v1_genomic.fna/markers.fasta
[2024-01-24 14:19:33,952] [INFO] Task started: Blastn
[2024-01-24 14:19:33,952] [INFO] Running command: blastn -query GCF_003263785.1_ASM326378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54ee0859-d1e7-496c-bf57-1f57b5c8bb47/dqc_reference/reference_markers.fasta -out GCF_003263785.1_ASM326378v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:34,792] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:34,796] [INFO] Selected 19 target genomes.
[2024-01-24 14:19:34,797] [INFO] Target genome list was writen to GCF_003263785.1_ASM326378v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:34,805] [INFO] Task started: fastANI
[2024-01-24 14:19:34,806] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4866c62-d435-4009-86c7-fe43817698f9/GCF_003263785.1_ASM326378v1_genomic.fna.gz --refList GCF_003263785.1_ASM326378v1_genomic.fna/target_genomes.txt --output GCF_003263785.1_ASM326378v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:52,457] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:52,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54ee0859-d1e7-496c-bf57-1f57b5c8bb47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:52,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54ee0859-d1e7-496c-bf57-1f57b5c8bb47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:52,475] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:52,475] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:52,476] [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 variabilis	strain=CAIM 1454	GCA_003263785.1	990271	990271	type	True	100.0	1620	1630	95	conclusive
Vibrio hangzhouensis	strain=CGMCC 1.7062	GCA_900107935.1	462991	462991	type	True	82.3439	666	1630	95	below_threshold
Vibrio mediterranei		GCA_900088415.1	689	689	type	True	81.8091	717	1630	95	below_threshold
Vibrio mediterranei	strain=NBRC 15635	GCA_001591125.1	689	689	type	True	81.7505	708	1630	95	below_threshold
Vibrio barjaei	strain=3062	GCA_001639065.2	1676683	1676683	type	True	81.6436	687	1630	95	below_threshold
Vibrio thalassae	strain=CECT8203	GCA_900089835.1	1243014	1243014	type	True	81.4053	643	1630	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.1964	390	1630	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.0072	385	1630	95	below_threshold
Vibrio maerlii	strain=G62	GCA_003415655.1	2231648	2231648	type	True	79.9418	351	1630	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	79.9262	356	1630	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.832	378	1630	95	below_threshold
Vibrio mexicanus	strain=CAIM 1540	GCA_001012815.1	1004326	1004326	type	True	79.8071	345	1630	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	79.6086	378	1630	95	below_threshold
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	79.5847	373	1630	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	79.5455	346	1630	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	79.5334	358	1630	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.5051	310	1630	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.3958	312	1630	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	79.0273	273	1630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:52,479] [INFO] DFAST Taxonomy check result was written to GCF_003263785.1_ASM326378v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:52,479] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:52,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:52,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54ee0859-d1e7-496c-bf57-1f57b5c8bb47/dqc_reference/checkm_data
[2024-01-24 14:19:52,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:52,541] [INFO] Task started: CheckM
[2024-01-24 14:19:52,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003263785.1_ASM326378v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003263785.1_ASM326378v1_genomic.fna/checkm_input GCF_003263785.1_ASM326378v1_genomic.fna/checkm_result
[2024-01-24 14:20:34,893] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:34,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:34,915] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:34,916] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:34,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003263785.1_ASM326378v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:34,917] [INFO] Task started: Blastn
[2024-01-24 14:20:34,917] [INFO] Running command: blastn -query GCF_003263785.1_ASM326378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54ee0859-d1e7-496c-bf57-1f57b5c8bb47/dqc_reference/reference_markers_gtdb.fasta -out GCF_003263785.1_ASM326378v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:36,122] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:36,125] [INFO] Selected 11 target genomes.
[2024-01-24 14:20:36,125] [INFO] Target genome list was writen to GCF_003263785.1_ASM326378v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:36,138] [INFO] Task started: fastANI
[2024-01-24 14:20:36,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4866c62-d435-4009-86c7-fe43817698f9/GCF_003263785.1_ASM326378v1_genomic.fna.gz --refList GCF_003263785.1_ASM326378v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003263785.1_ASM326378v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:47,409] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:47,427] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:47,427] [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
GCA_003263785.1	s__Vibrio variabilis	100.0	1620	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003263775.1	s__Vibrio maritimus	93.536	1393	1630	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	92.6176	1365	1630	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	85.4135	1005	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.88	95.88	0.85	0.85	2	-
GCF_900107935.1	s__Vibrio hangzhouensis	82.3429	667	1630	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	81.8032	719	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.1582	98.19	97.23	0.91	0.86	13	-
GCF_900089835.1	s__Vibrio thalassae	81.405	643	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.8081	N/A	N/A	N/A	N/A	1	-
GCA_000695745.1	s__Vibrio madracius	81.3609	305	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.8081	N/A	N/A	N/A	N/A	1	-
GCF_001012815.1	s__Vibrio mexicanus	79.8221	344	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013114545.1	s__Vibrio sp013114545	79.8127	353	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350325.1	s__Vibrio rhodolitus	79.6073	340	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:47,429] [INFO] GTDB search result was written to GCF_003263785.1_ASM326378v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:47,430] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:47,435] [INFO] DFAST_QC result json was written to GCF_003263785.1_ASM326378v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:47,435] [INFO] DFAST_QC completed!
[2024-01-24 14:20:47,435] [INFO] Total running time: 0h1m29s