[2024-01-24 13:49:29,348] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:29,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:29,351] [INFO] DQC Reference Directory: /var/lib/cwl/stga4e58801-92f9-475f-ae15-2243614de268/dqc_reference
[2024-01-24 13:49:30,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:30,775] [INFO] Task started: Prodigal
[2024-01-24 13:49:30,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bac6a51-fa0d-46de-ba6f-0fce00e51dec/GCF_006538525.1_ASM653852v1_genomic.fna.gz | prodigal -d GCF_006538525.1_ASM653852v1_genomic.fna/cds.fna -a GCF_006538525.1_ASM653852v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:40,675] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:40,676] [INFO] Task started: HMMsearch
[2024-01-24 13:49:40,676] [INFO] Running command: hmmsearch --tblout GCF_006538525.1_ASM653852v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4e58801-92f9-475f-ae15-2243614de268/dqc_reference/reference_markers.hmm GCF_006538525.1_ASM653852v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:41,045] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:41,046] [INFO] Found 6/6 markers.
[2024-01-24 13:49:41,097] [INFO] Query marker FASTA was written to GCF_006538525.1_ASM653852v1_genomic.fna/markers.fasta
[2024-01-24 13:49:41,098] [INFO] Task started: Blastn
[2024-01-24 13:49:41,098] [INFO] Running command: blastn -query GCF_006538525.1_ASM653852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4e58801-92f9-475f-ae15-2243614de268/dqc_reference/reference_markers.fasta -out GCF_006538525.1_ASM653852v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:42,083] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:42,086] [INFO] Selected 10 target genomes.
[2024-01-24 13:49:42,086] [INFO] Target genome list was writen to GCF_006538525.1_ASM653852v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:42,091] [INFO] Task started: fastANI
[2024-01-24 13:49:42,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bac6a51-fa0d-46de-ba6f-0fce00e51dec/GCF_006538525.1_ASM653852v1_genomic.fna.gz --refList GCF_006538525.1_ASM653852v1_genomic.fna/target_genomes.txt --output GCF_006538525.1_ASM653852v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:51,713] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:51,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4e58801-92f9-475f-ae15-2243614de268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:51,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4e58801-92f9-475f-ae15-2243614de268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:51,723] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:51,723] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:51,723] [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 inusitatus	strain=NBRC 102082	GCA_006538525.1	413402	413402	type	True	100.0	1428	1428	95	conclusive
Vibrio inusitatus	strain=LMG 23434	GCA_024346935.1	413402	413402	type	True	99.999	1427	1428	95	conclusive
Vibrio comitans	strain=LMG 23416	GCA_024346835.1	413401	413401	type	True	88.1967	1096	1428	95	below_threshold
Vibrio comitans	strain=NBRC 102076	GCA_006538565.1	413401	413401	type	True	88.1957	1082	1428	95	below_threshold
Vibrio superstes	strain=G3-29	GCA_003569005.1	198815	198815	type	True	86.4262	1057	1428	95	below_threshold
Vibrio superstes	strain=NBRC 103154	GCA_007990955.1	198815	198815	type	True	86.3758	1029	1428	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	81.1957	515	1428	95	below_threshold
Vibrio halioticoli	strain=NBRC 102217	GCA_000496695.1	71388	71388	type	True	81.0456	525	1428	95	below_threshold
Vibrio gallicus	strain=CIP 107863	GCA_024346875.1	190897	190897	type	True	80.2055	333	1428	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.0365	212	1428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:51,725] [INFO] DFAST Taxonomy check result was written to GCF_006538525.1_ASM653852v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:51,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:51,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:51,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4e58801-92f9-475f-ae15-2243614de268/dqc_reference/checkm_data
[2024-01-24 13:49:51,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:51,774] [INFO] Task started: CheckM
[2024-01-24 13:49:51,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006538525.1_ASM653852v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006538525.1_ASM653852v1_genomic.fna/checkm_input GCF_006538525.1_ASM653852v1_genomic.fna/checkm_result
[2024-01-24 13:50:28,422] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:28,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:28,471] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:28,471] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:28,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006538525.1_ASM653852v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:28,472] [INFO] Task started: Blastn
[2024-01-24 13:50:28,472] [INFO] Running command: blastn -query GCF_006538525.1_ASM653852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4e58801-92f9-475f-ae15-2243614de268/dqc_reference/reference_markers_gtdb.fasta -out GCF_006538525.1_ASM653852v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:29,652] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:29,656] [INFO] Selected 7 target genomes.
[2024-01-24 13:50:29,657] [INFO] Target genome list was writen to GCF_006538525.1_ASM653852v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:29,663] [INFO] Task started: fastANI
[2024-01-24 13:50:29,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bac6a51-fa0d-46de-ba6f-0fce00e51dec/GCF_006538525.1_ASM653852v1_genomic.fna.gz --refList GCF_006538525.1_ASM653852v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006538525.1_ASM653852v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:36,548] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:36,561] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:36,561] [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_006538525.1	s__Vibrio inusitatus	100.0	1428	1428	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_006538565.1	s__Vibrio comitans	88.1957	1082	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677275.1	s__Vibrio breoganii	86.6696	1044	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.22	96.88	0.90	0.86	59	-
GCF_003569005.1	s__Vibrio superstes	86.42	1058	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000467185.1	s__Vibrio ezurae	81.0836	542	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000496695.1	s__Vibrio halioticoli	81.0374	526	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.31	0.94	0.87	3	-
GCF_001676025.1	s__Vibrio sp001676025	80.9034	564	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:36,573] [INFO] GTDB search result was written to GCF_006538525.1_ASM653852v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:36,574] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:36,579] [INFO] DFAST_QC result json was written to GCF_006538525.1_ASM653852v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:36,579] [INFO] DFAST_QC completed!
[2024-01-24 13:50:36,579] [INFO] Total running time: 0h1m7s