[2024-01-24 13:49:45,271] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,273] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,273] [INFO] DQC Reference Directory: /var/lib/cwl/stg4408e5be-9513-4f09-a1a7-4761b69728cc/dqc_reference
[2024-01-24 13:49:46,666] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,666] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,667] [INFO] Running command: gunzip -c /var/lib/cwl/stg2647bd56-d374-40b5-a39f-b6cba27de796/GCF_018736065.1_ASM1873606v1_genomic.fna.gz | prodigal -d GCF_018736065.1_ASM1873606v1_genomic.fna/cds.fna -a GCF_018736065.1_ASM1873606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:06,885] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:06,885] [INFO] Task started: HMMsearch
[2024-01-24 13:50:06,886] [INFO] Running command: hmmsearch --tblout GCF_018736065.1_ASM1873606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4408e5be-9513-4f09-a1a7-4761b69728cc/dqc_reference/reference_markers.hmm GCF_018736065.1_ASM1873606v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:07,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:07,225] [INFO] Found 6/6 markers.
[2024-01-24 13:50:07,276] [INFO] Query marker FASTA was written to GCF_018736065.1_ASM1873606v1_genomic.fna/markers.fasta
[2024-01-24 13:50:07,276] [INFO] Task started: Blastn
[2024-01-24 13:50:07,276] [INFO] Running command: blastn -query GCF_018736065.1_ASM1873606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4408e5be-9513-4f09-a1a7-4761b69728cc/dqc_reference/reference_markers.fasta -out GCF_018736065.1_ASM1873606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:07,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:07,887] [INFO] Selected 9 target genomes.
[2024-01-24 13:50:07,887] [INFO] Target genome list was writen to GCF_018736065.1_ASM1873606v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:07,891] [INFO] Task started: fastANI
[2024-01-24 13:50:07,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg2647bd56-d374-40b5-a39f-b6cba27de796/GCF_018736065.1_ASM1873606v1_genomic.fna.gz --refList GCF_018736065.1_ASM1873606v1_genomic.fna/target_genomes.txt --output GCF_018736065.1_ASM1873606v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:19,899] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:19,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4408e5be-9513-4f09-a1a7-4761b69728cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:19,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4408e5be-9513-4f09-a1a7-4761b69728cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:19,911] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:50:19,912] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:19,912] [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_018736065.1	373891	373891	type	True	100.0	2318	2320	95	conclusive
Flammeovirga kamogawensis	strain=YS10	GCA_007097495.1	373891	373891	type	True	99.9954	2313	2320	95	conclusive
Flammeovirga kamogawensis	strain=DSM 26273	GCA_014207545.1	373891	373891	type	True	99.9674	2259	2320	95	conclusive
Flammeovirga pectinis	strain=L12M1	GCA_003970675.1	2494373	2494373	type	True	89.3375	1922	2320	95	below_threshold
Flammeovirga aprica	strain=ATCC 23126	GCA_012844305.1	29528	29528	type	True	78.5818	588	2320	95	below_threshold
Flammeovirga pacifica	strain=WPAGA1	GCA_000807855.2	915059	915059	type	True	78.4001	604	2320	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.2493	65	2320	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:19,913] [INFO] DFAST Taxonomy check result was written to GCF_018736065.1_ASM1873606v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:19,914] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:19,914] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:19,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4408e5be-9513-4f09-a1a7-4761b69728cc/dqc_reference/checkm_data
[2024-01-24 13:50:19,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:19,986] [INFO] Task started: CheckM
[2024-01-24 13:50:19,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018736065.1_ASM1873606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018736065.1_ASM1873606v1_genomic.fna/checkm_input GCF_018736065.1_ASM1873606v1_genomic.fna/checkm_result
[2024-01-24 13:51:17,133] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:17,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:17,158] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:17,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:17,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018736065.1_ASM1873606v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:17,159] [INFO] Task started: Blastn
[2024-01-24 13:51:17,159] [INFO] Running command: blastn -query GCF_018736065.1_ASM1873606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4408e5be-9513-4f09-a1a7-4761b69728cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_018736065.1_ASM1873606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:17,919] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:17,923] [INFO] Selected 12 target genomes.
[2024-01-24 13:51:17,923] [INFO] Target genome list was writen to GCF_018736065.1_ASM1873606v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:17,950] [INFO] Task started: fastANI
[2024-01-24 13:51:17,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg2647bd56-d374-40b5-a39f-b6cba27de796/GCF_018736065.1_ASM1873606v1_genomic.fna.gz --refList GCF_018736065.1_ASM1873606v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018736065.1_ASM1873606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:32,605] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:32,619] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:32,619] [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	100.0	2317	2320	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	89.3443	1920	2320	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	78.5984	584	2320	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	78.5247	616	2320	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	78.4499	602	2320	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	78.4296	604	2320	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	78.391	606	2320	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	78.3184	677	2320	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	76.094	64	2320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188275.1	s__Dokdonia pacifica	75.0007	55	2320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:32,621] [INFO] GTDB search result was written to GCF_018736065.1_ASM1873606v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:32,622] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:32,625] [INFO] DFAST_QC result json was written to GCF_018736065.1_ASM1873606v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:32,625] [INFO] DFAST_QC completed!
[2024-01-24 13:51:32,625] [INFO] Total running time: 0h1m47s