[2024-01-24 13:55:25,675] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:25,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:25,678] [INFO] DQC Reference Directory: /var/lib/cwl/stgb14ecade-620a-4437-a866-fba9bc7c1691/dqc_reference
[2024-01-24 13:55:26,987] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:26,988] [INFO] Task started: Prodigal
[2024-01-24 13:55:26,988] [INFO] Running command: gunzip -c /var/lib/cwl/stg05330d72-81d0-47bf-86b5-ea824302b08b/GCF_007097495.1_ASM709749v1_genomic.fna.gz | prodigal -d GCF_007097495.1_ASM709749v1_genomic.fna/cds.fna -a GCF_007097495.1_ASM709749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:46,900] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:46,901] [INFO] Task started: HMMsearch
[2024-01-24 13:55:46,901] [INFO] Running command: hmmsearch --tblout GCF_007097495.1_ASM709749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb14ecade-620a-4437-a866-fba9bc7c1691/dqc_reference/reference_markers.hmm GCF_007097495.1_ASM709749v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:47,229] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:47,231] [INFO] Found 6/6 markers.
[2024-01-24 13:55:47,288] [INFO] Query marker FASTA was written to GCF_007097495.1_ASM709749v1_genomic.fna/markers.fasta
[2024-01-24 13:55:47,288] [INFO] Task started: Blastn
[2024-01-24 13:55:47,288] [INFO] Running command: blastn -query GCF_007097495.1_ASM709749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb14ecade-620a-4437-a866-fba9bc7c1691/dqc_reference/reference_markers.fasta -out GCF_007097495.1_ASM709749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:47,873] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:47,877] [INFO] Selected 9 target genomes.
[2024-01-24 13:55:47,877] [INFO] Target genome list was writen to GCF_007097495.1_ASM709749v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:47,938] [INFO] Task started: fastANI
[2024-01-24 13:55:47,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg05330d72-81d0-47bf-86b5-ea824302b08b/GCF_007097495.1_ASM709749v1_genomic.fna.gz --refList GCF_007097495.1_ASM709749v1_genomic.fna/target_genomes.txt --output GCF_007097495.1_ASM709749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:59,897] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:59,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb14ecade-620a-4437-a866-fba9bc7c1691/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:59,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb14ecade-620a-4437-a866-fba9bc7c1691/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:59,904] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:55:59,905] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:59,905] [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
Flammeovirga kamogawensis	strain=YS10	GCA_007097495.1	373891	373891	type	True	100.0	2322	2322	95	conclusive
Flammeovirga kamogawensis	strain=YS10	GCA_018736065.1	373891	373891	type	True	99.9955	2314	2322	95	conclusive
Flammeovirga kamogawensis	strain=DSM 26273	GCA_014207545.1	373891	373891	type	True	99.9774	2251	2322	95	conclusive
Flammeovirga pectinis	strain=L12M1	GCA_003970675.1	2494373	2494373	type	True	89.4005	1924	2322	95	below_threshold
Flammeovirga aprica	strain=ATCC 23126	GCA_012844305.1	29528	29528	type	True	78.562	575	2322	95	below_threshold
Flammeovirga pacifica	strain=WPAGA1	GCA_000807855.2	915059	915059	type	True	78.2838	622	2322	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.3024	63	2322	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:59,908] [INFO] DFAST Taxonomy check result was written to GCF_007097495.1_ASM709749v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:59,909] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:59,909] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:59,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb14ecade-620a-4437-a866-fba9bc7c1691/dqc_reference/checkm_data
[2024-01-24 13:55:59,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:59,978] [INFO] Task started: CheckM
[2024-01-24 13:55:59,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007097495.1_ASM709749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007097495.1_ASM709749v1_genomic.fna/checkm_input GCF_007097495.1_ASM709749v1_genomic.fna/checkm_result
[2024-01-24 13:56:57,141] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:57,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:57,163] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:57,164] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:57,164] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007097495.1_ASM709749v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:57,165] [INFO] Task started: Blastn
[2024-01-24 13:56:57,165] [INFO] Running command: blastn -query GCF_007097495.1_ASM709749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb14ecade-620a-4437-a866-fba9bc7c1691/dqc_reference/reference_markers_gtdb.fasta -out GCF_007097495.1_ASM709749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:57,950] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:57,954] [INFO] Selected 12 target genomes.
[2024-01-24 13:56:57,955] [INFO] Target genome list was writen to GCF_007097495.1_ASM709749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:58,043] [INFO] Task started: fastANI
[2024-01-24 13:56:58,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg05330d72-81d0-47bf-86b5-ea824302b08b/GCF_007097495.1_ASM709749v1_genomic.fna.gz --refList GCF_007097495.1_ASM709749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007097495.1_ASM709749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:15,178] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:15,191] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:15,192] [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_018736065.1	s__Flammeovirga kamogawensis	99.9955	2314	2322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_003970675.1	s__Flammeovirga pectinis	89.4161	1922	2322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012844305.1	s__Flammeovirga aprica	78.5516	576	2322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812565.1	s__Flammeovirga sp000812565	78.5437	613	2322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583495.1	s__Flammeovirga sp001583495	78.4934	586	2322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534745.1	s__Flammeovirga sp014534745	78.4095	615	2322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641475.1	s__Flammeovirga sp012641475	78.3725	682	2322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000807855.2	s__Flammeovirga pacifica	78.2817	623	2322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	76.3143	63	2322	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:15,193] [INFO] GTDB search result was written to GCF_007097495.1_ASM709749v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:15,194] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:15,196] [INFO] DFAST_QC result json was written to GCF_007097495.1_ASM709749v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:15,197] [INFO] DFAST_QC completed!
[2024-01-24 13:57:15,197] [INFO] Total running time: 0h1m50s