[2023-06-16 21:40:33,173] [INFO] DFAST_QC pipeline started.
[2023-06-16 21:40:33,176] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 21:40:33,176] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b8355bc-8b66-4b96-b5bf-686759ac8751/dqc_reference
[2023-06-16 21:40:34,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 21:40:34,518] [INFO] Task started: Prodigal
[2023-06-16 21:40:34,518] [INFO] Running command: gunzip -c /var/lib/cwl/stg42826025-80a5-461c-bfa7-32234eeec51d/GCA_013372875.1_ASM1337287v1_genomic.fna.gz | prodigal -d GCA_013372875.1_ASM1337287v1_genomic.fna/cds.fna -a GCA_013372875.1_ASM1337287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 21:40:43,042] [INFO] Task succeeded: Prodigal
[2023-06-16 21:40:43,042] [INFO] Task started: HMMsearch
[2023-06-16 21:40:43,043] [INFO] Running command: hmmsearch --tblout GCA_013372875.1_ASM1337287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b8355bc-8b66-4b96-b5bf-686759ac8751/dqc_reference/reference_markers.hmm GCA_013372875.1_ASM1337287v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 21:40:43,334] [INFO] Task succeeded: HMMsearch
[2023-06-16 21:40:43,338] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg42826025-80a5-461c-bfa7-32234eeec51d/GCA_013372875.1_ASM1337287v1_genomic.fna.gz]
[2023-06-16 21:40:43,387] [INFO] Query marker FASTA was written to GCA_013372875.1_ASM1337287v1_genomic.fna/markers.fasta
[2023-06-16 21:40:43,387] [INFO] Task started: Blastn
[2023-06-16 21:40:43,387] [INFO] Running command: blastn -query GCA_013372875.1_ASM1337287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b8355bc-8b66-4b96-b5bf-686759ac8751/dqc_reference/reference_markers.fasta -out GCA_013372875.1_ASM1337287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:40:44,072] [INFO] Task succeeded: Blastn
[2023-06-16 21:40:44,077] [INFO] Selected 31 target genomes.
[2023-06-16 21:40:44,078] [INFO] Target genome list was writen to GCA_013372875.1_ASM1337287v1_genomic.fna/target_genomes.txt
[2023-06-16 21:40:44,098] [INFO] Task started: fastANI
[2023-06-16 21:40:44,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg42826025-80a5-461c-bfa7-32234eeec51d/GCA_013372875.1_ASM1337287v1_genomic.fna.gz --refList GCA_013372875.1_ASM1337287v1_genomic.fna/target_genomes.txt --output GCA_013372875.1_ASM1337287v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 21:41:03,200] [INFO] Task succeeded: fastANI
[2023-06-16 21:41:03,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b8355bc-8b66-4b96-b5bf-686759ac8751/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 21:41:03,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b8355bc-8b66-4b96-b5bf-686759ac8751/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 21:41:03,212] [INFO] Found 12 fastANI hits (5 hits with ANI > threshold)
[2023-06-16 21:41:03,212] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-16 21:41:03,212] [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 parahaemolyticus	strain=ATCC 17802	GCA_001998785.1	670	670	type	True	97.1916	379	1106	95	conclusive
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	97.1709	379	1106	95	conclusive
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	97.1568	380	1106	95	conclusive
Vibrio parahaemolyticus		GCA_001558495.2	670	670	type	True	97.0878	381	1106	95	conclusive
Vibrio parahaemolyticus	strain=NBRC 12711	GCA_000813305.1	670	670	type	True	97.075	374	1106	95	conclusive
Kangiella sediminilitoris	strain=KCTC 23892	GCA_001708405.1	1144748	1144748	type	True	76.3234	59	1106	95	below_threshold
Kangiella spongicola	strain=ATCC BAA-2076	GCA_003194565.2	796379	796379	type	True	76.2796	73	1106	95	below_threshold
Kangiella taiwanensis	strain=KT1	GCA_020005165.1	1079179	1079179	type	True	76.2375	73	1106	95	below_threshold
Kangiella shandongensis	strain=PI	GCA_020005365.1	2763258	2763258	type	True	76.1605	53	1106	95	below_threshold
Kangiella koreensis	strain=DSM 16069	GCA_000024085.1	261964	261964	type	True	76.1358	82	1106	95	below_threshold
Kangiella profundi	strain=CGMCC 1.12959	GCA_014640235.1	1561924	1561924	type	True	76.034	73	1106	95	below_threshold
Kangiella aquimarina	strain=DSM 16071	GCA_000374105.1	261965	261965	type	True	75.7922	74	1106	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 21:41:03,214] [INFO] DFAST Taxonomy check result was written to GCA_013372875.1_ASM1337287v1_genomic.fna/tc_result.tsv
[2023-06-16 21:41:03,215] [INFO] ===== Taxonomy check completed =====
[2023-06-16 21:41:03,215] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 21:41:03,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b8355bc-8b66-4b96-b5bf-686759ac8751/dqc_reference/checkm_data
[2023-06-16 21:41:03,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 21:41:03,278] [INFO] Task started: CheckM
[2023-06-16 21:41:03,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013372875.1_ASM1337287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013372875.1_ASM1337287v1_genomic.fna/checkm_input GCA_013372875.1_ASM1337287v1_genomic.fna/checkm_result
[2023-06-16 21:41:35,196] [INFO] Task succeeded: CheckM
[2023-06-16 21:41:35,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:41:35,219] [INFO] ===== Completeness check finished =====
[2023-06-16 21:41:35,220] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:41:35,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013372875.1_ASM1337287v1_genomic.fna/markers.fasta)
[2023-06-16 21:41:35,221] [INFO] Task started: Blastn
[2023-06-16 21:41:35,221] [INFO] Running command: blastn -query GCA_013372875.1_ASM1337287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b8355bc-8b66-4b96-b5bf-686759ac8751/dqc_reference/reference_markers_gtdb.fasta -out GCA_013372875.1_ASM1337287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:41:36,237] [INFO] Task succeeded: Blastn
[2023-06-16 21:41:36,242] [INFO] Selected 25 target genomes.
[2023-06-16 21:41:36,242] [INFO] Target genome list was writen to GCA_013372875.1_ASM1337287v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:41:36,265] [INFO] Task started: fastANI
[2023-06-16 21:41:36,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg42826025-80a5-461c-bfa7-32234eeec51d/GCA_013372875.1_ASM1337287v1_genomic.fna.gz --refList GCA_013372875.1_ASM1337287v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013372875.1_ASM1337287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:41:51,560] [INFO] Task succeeded: fastANI
[2023-06-16 21:41:51,583] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-16 21:41:51,583] [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_013372875.1	s__Kangiella sp013372875	100.0	1086	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_900460535.1	s__Vibrio parahaemolyticus	97.1568	380	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	inconclusive
GCF_000354175.2	s__Vibrio alginolyticus	83.0599	250	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_009674675.1	s__Kangiella sp009674675	78.6406	241	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400365.1	s__Vibrio jasicida	77.3861	120	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_002906655.1	s__Vibrio hyugaensis	77.1511	120	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCA_013373015.1	s__Kangiella sp013373015	76.8668	149	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001708405.1	s__Kangiella sediminilitoris	76.3234	59	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981765.1	s__Kangiella geojedonensis	76.1648	63	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024085.1	s__Kangiella koreensis	76.1474	83	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762745.1	s__Kangiella sp014762745	75.8913	74	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374105.1	s__Kangiella aquimarina	75.7922	74	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 21:41:51,587] [INFO] GTDB search result was written to GCA_013372875.1_ASM1337287v1_genomic.fna/result_gtdb.tsv
[2023-06-16 21:41:51,587] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:41:51,592] [INFO] DFAST_QC result json was written to GCA_013372875.1_ASM1337287v1_genomic.fna/dqc_result.json
[2023-06-16 21:41:51,592] [INFO] DFAST_QC completed!
[2023-06-16 21:41:51,592] [INFO] Total running time: 0h1m18s