[2024-01-24 13:37:05,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg3db50497-48d8-484c-ba40-8846e2e2ed9c/dqc_reference
[2024-01-24 13:37:06,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,736] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg33a664a4-1480-4dc3-8c5d-f38b6c51515d/GCF_000621645.1_ASM62164v1_genomic.fna.gz | prodigal -d GCF_000621645.1_ASM62164v1_genomic.fna/cds.fna -a GCF_000621645.1_ASM62164v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:18,005] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:18,006] [INFO] Task started: HMMsearch
[2024-01-24 13:37:18,006] [INFO] Running command: hmmsearch --tblout GCF_000621645.1_ASM62164v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3db50497-48d8-484c-ba40-8846e2e2ed9c/dqc_reference/reference_markers.hmm GCF_000621645.1_ASM62164v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:18,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:18,359] [INFO] Found 6/6 markers.
[2024-01-24 13:37:18,406] [INFO] Query marker FASTA was written to GCF_000621645.1_ASM62164v1_genomic.fna/markers.fasta
[2024-01-24 13:37:18,406] [INFO] Task started: Blastn
[2024-01-24 13:37:18,406] [INFO] Running command: blastn -query GCF_000621645.1_ASM62164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3db50497-48d8-484c-ba40-8846e2e2ed9c/dqc_reference/reference_markers.fasta -out GCF_000621645.1_ASM62164v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:19,320] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:19,323] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:19,323] [INFO] Target genome list was writen to GCF_000621645.1_ASM62164v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:19,326] [INFO] Task started: fastANI
[2024-01-24 13:37:19,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg33a664a4-1480-4dc3-8c5d-f38b6c51515d/GCF_000621645.1_ASM62164v1_genomic.fna.gz --refList GCF_000621645.1_ASM62164v1_genomic.fna/target_genomes.txt --output GCF_000621645.1_ASM62164v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:31,079] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:31,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3db50497-48d8-484c-ba40-8846e2e2ed9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:31,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3db50497-48d8-484c-ba40-8846e2e2ed9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:31,090] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:37:31,091] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:37:31,091] [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 cholerae	strain=ATCC 14035	GCA_000621645.1	666	666	type	True	100.0	1308	1313	95	inconclusive
Vibrio paracholerae	strain=EDC-792	GCA_017169525.1	650003	650003	type	True	95.951	1119	1313	95	inconclusive
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	95.3728	1122	1313	95	inconclusive
Vibrio metoecus	strain=OP3H	GCA_000696385.1	1481663	1481663	type	True	88.4605	1030	1313	95	below_threshold
Vibrio mimicus	strain=CAIM 602	GCA_000338875.1	674	674	type	True	86.483	1013	1313	95	below_threshold
Vibrio mimicus	strain=NCTC11435	GCA_900460385.1	674	674	type	True	86.4532	1038	1313	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.5053	306	1313	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	78.4823	283	1313	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.4664	310	1313	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	78.3069	304	1313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:31,096] [INFO] DFAST Taxonomy check result was written to GCF_000621645.1_ASM62164v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:31,097] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:31,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:31,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3db50497-48d8-484c-ba40-8846e2e2ed9c/dqc_reference/checkm_data
[2024-01-24 13:37:31,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:31,150] [INFO] Task started: CheckM
[2024-01-24 13:37:31,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621645.1_ASM62164v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621645.1_ASM62164v1_genomic.fna/checkm_input GCF_000621645.1_ASM62164v1_genomic.fna/checkm_result
[2024-01-24 13:38:10,581] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:10,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:10,600] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:10,601] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:10,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621645.1_ASM62164v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:10,602] [INFO] Task started: Blastn
[2024-01-24 13:38:10,602] [INFO] Running command: blastn -query GCF_000621645.1_ASM62164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3db50497-48d8-484c-ba40-8846e2e2ed9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621645.1_ASM62164v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:11,897] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:11,900] [INFO] Selected 5 target genomes.
[2024-01-24 13:38:11,901] [INFO] Target genome list was writen to GCF_000621645.1_ASM62164v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:11,906] [INFO] Task started: fastANI
[2024-01-24 13:38:11,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg33a664a4-1480-4dc3-8c5d-f38b6c51515d/GCF_000621645.1_ASM62164v1_genomic.fna.gz --refList GCF_000621645.1_ASM62164v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621645.1_ASM62164v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:18,046] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:18,052] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:18,052] [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_001471585.2	s__Vibrio cholerae	97.7443	1175	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.72	95.09	0.90	0.82	1544	conclusive
GCF_009665255.1	s__Vibrio metoecus_B	89.3663	1057	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.11	98.11	0.94	0.94	2	-
GCF_000696385.1	s__Vibrio metoecus	88.4548	1031	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.79	97.58	0.93	0.89	26	-
GCF_019048845.1	s__Vibrio sp000176715	88.1901	1033	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.20	96.20	0.92	0.92	2	-
GCF_000338875.1	s__Vibrio mimicus	86.5062	1010	1313	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 13:38:18,054] [INFO] GTDB search result was written to GCF_000621645.1_ASM62164v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:18,054] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:18,057] [INFO] DFAST_QC result json was written to GCF_000621645.1_ASM62164v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:18,057] [INFO] DFAST_QC completed!
[2024-01-24 13:38:18,057] [INFO] Total running time: 0h1m13s