[2024-01-24 12:22:26,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:26,432] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:26,432] [INFO] DQC Reference Directory: /var/lib/cwl/stga75aee8b-2fd2-4453-b283-f2c66e757fa8/dqc_reference
[2024-01-24 12:22:27,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:27,731] [INFO] Task started: Prodigal
[2024-01-24 12:22:27,731] [INFO] Running command: gunzip -c /var/lib/cwl/stg4acc47a3-bfaf-4511-9972-82bcc4a25d63/GCF_001558415.2_ASM155841v2_genomic.fna.gz | prodigal -d GCF_001558415.2_ASM155841v2_genomic.fna/cds.fna -a GCF_001558415.2_ASM155841v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:42,067] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:42,067] [INFO] Task started: HMMsearch
[2024-01-24 12:22:42,067] [INFO] Running command: hmmsearch --tblout GCF_001558415.2_ASM155841v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga75aee8b-2fd2-4453-b283-f2c66e757fa8/dqc_reference/reference_markers.hmm GCF_001558415.2_ASM155841v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:42,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:42,433] [INFO] Found 6/6 markers.
[2024-01-24 12:22:42,481] [INFO] Query marker FASTA was written to GCF_001558415.2_ASM155841v2_genomic.fna/markers.fasta
[2024-01-24 12:22:42,482] [INFO] Task started: Blastn
[2024-01-24 12:22:42,482] [INFO] Running command: blastn -query GCF_001558415.2_ASM155841v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga75aee8b-2fd2-4453-b283-f2c66e757fa8/dqc_reference/reference_markers.fasta -out GCF_001558415.2_ASM155841v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:43,365] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:43,387] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:43,388] [INFO] Target genome list was writen to GCF_001558415.2_ASM155841v2_genomic.fna/target_genomes.txt
[2024-01-24 12:22:43,393] [INFO] Task started: fastANI
[2024-01-24 12:22:43,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg4acc47a3-bfaf-4511-9972-82bcc4a25d63/GCF_001558415.2_ASM155841v2_genomic.fna.gz --refList GCF_001558415.2_ASM155841v2_genomic.fna/target_genomes.txt --output GCF_001558415.2_ASM155841v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:53,969] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:53,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga75aee8b-2fd2-4453-b283-f2c66e757fa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:53,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga75aee8b-2fd2-4453-b283-f2c66e757fa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:53,981] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:22:53,981] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:53,981] [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 fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	100.0	1605	1608	95	conclusive
Vibrio fluvialis	strain=NCTC11327	GCA_900460245.1	676	676	type	True	99.9996	1608	1608	95	conclusive
Vibrio fluvialis	strain=NBRC 103150	GCA_001598835.1	676	676	type	True	99.9816	1563	1608	95	conclusive
Vibrio furnissii	strain=FDAARGOS_777	GCA_006364355.1	29494	29494	type	True	87.7173	1295	1608	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	87.7145	1310	1608	95	below_threshold
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	87.6802	1275	1608	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	79.8815	545	1608	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	79.3367	342	1608	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	79.2493	366	1608	95	below_threshold
Vibrio albus	strain=E4404	GCA_003144035.1	2200953	2200953	type	True	78.8886	234	1608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:53,984] [INFO] DFAST Taxonomy check result was written to GCF_001558415.2_ASM155841v2_genomic.fna/tc_result.tsv
[2024-01-24 12:22:53,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:53,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:53,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga75aee8b-2fd2-4453-b283-f2c66e757fa8/dqc_reference/checkm_data
[2024-01-24 12:22:53,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:54,042] [INFO] Task started: CheckM
[2024-01-24 12:22:54,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001558415.2_ASM155841v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001558415.2_ASM155841v2_genomic.fna/checkm_input GCF_001558415.2_ASM155841v2_genomic.fna/checkm_result
[2024-01-24 12:23:40,392] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:40,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:40,422] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:40,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:40,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001558415.2_ASM155841v2_genomic.fna/markers.fasta)
[2024-01-24 12:23:40,423] [INFO] Task started: Blastn
[2024-01-24 12:23:40,424] [INFO] Running command: blastn -query GCF_001558415.2_ASM155841v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga75aee8b-2fd2-4453-b283-f2c66e757fa8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001558415.2_ASM155841v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:41,726] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:41,730] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:41,730] [INFO] Target genome list was writen to GCF_001558415.2_ASM155841v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:41,744] [INFO] Task started: fastANI
[2024-01-24 12:23:41,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg4acc47a3-bfaf-4511-9972-82bcc4a25d63/GCF_001558415.2_ASM155841v2_genomic.fna.gz --refList GCF_001558415.2_ASM155841v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001558415.2_ASM155841v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:56,367] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:56,393] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:56,394] [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_900460245.1	s__Vibrio fluvialis	99.9996	1607	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	conclusive
GCF_000176175.1	s__Vibrio furnissii	87.6933	1275	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_019226825.1	s__Vibrio sp004804295	81.9598	832	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.23	99.23	0.93	0.93	2	-
GCF_000764325.1	s__Vibrio navarrensis	80.4868	474	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.19	97.06	0.93	0.87	22	-
GCF_011064285.1	s__Vibrio ziniensis	80.1974	492	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015767675.1	s__Vibrio sp000960595	80.1766	470	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.38	0.94	0.90	8	-
GCF_013041605.1	s__Vibrio plantisponsor	80.1585	548	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.35	98.35	0.93	0.93	2	-
GCF_009763805.1	s__Vibrio cidicii	80.1483	464	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.20	97.77	0.90	0.87	8	-
GCF_019048845.1	s__Vibrio sp000176715	79.9083	518	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.20	96.20	0.92	0.92	2	-
GCF_014596725.1	s__Vibrio sp014596725	79.8801	516	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.52	0.94	0.94	2	-
GCF_009665255.1	s__Vibrio metoecus_B	79.8733	518	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.11	98.11	0.94	0.94	2	-
GCF_905175385.1	s__Vibrio sp903986855	79.6387	400	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.95	0.95	0.92	4	-
GCF_900167345.1	s__Vibrio cincinnatiensis	79.5794	400	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	99.06	0.97	0.94	6	-
GCF_002749895.1	s__Vibrio fujianensis	79.5749	338	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.21	99.14	0.95	0.93	8	-
GCF_000338875.1	s__Vibrio mimicus	79.5725	506	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.81	0.94	0.91	26	-
GCA_001048675.1	s__Vibrio diabolicus	79.1483	384	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:56,395] [INFO] GTDB search result was written to GCF_001558415.2_ASM155841v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:56,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:56,401] [INFO] DFAST_QC result json was written to GCF_001558415.2_ASM155841v2_genomic.fna/dqc_result.json
[2024-01-24 12:23:56,401] [INFO] DFAST_QC completed!
[2024-01-24 12:23:56,401] [INFO] Total running time: 0h1m30s