[2024-01-24 14:55:08,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,654] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,654] [INFO] DQC Reference Directory: /var/lib/cwl/stg63a36318-47ed-4478-ac36-5628501b35ce/dqc_reference
[2024-01-24 14:55:10,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:10,178] [INFO] Task started: Prodigal
[2024-01-24 14:55:10,178] [INFO] Running command: gunzip -c /var/lib/cwl/stgd16ed542-af57-4dd7-9b3d-356f636ca660/GCF_003970675.1_ASM397067v1_genomic.fna.gz | prodigal -d GCF_003970675.1_ASM397067v1_genomic.fna/cds.fna -a GCF_003970675.1_ASM397067v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:29,158] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:29,159] [INFO] Task started: HMMsearch
[2024-01-24 14:55:29,159] [INFO] Running command: hmmsearch --tblout GCF_003970675.1_ASM397067v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63a36318-47ed-4478-ac36-5628501b35ce/dqc_reference/reference_markers.hmm GCF_003970675.1_ASM397067v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:29,478] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:29,479] [INFO] Found 6/6 markers.
[2024-01-24 14:55:29,533] [INFO] Query marker FASTA was written to GCF_003970675.1_ASM397067v1_genomic.fna/markers.fasta
[2024-01-24 14:55:29,534] [INFO] Task started: Blastn
[2024-01-24 14:55:29,534] [INFO] Running command: blastn -query GCF_003970675.1_ASM397067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63a36318-47ed-4478-ac36-5628501b35ce/dqc_reference/reference_markers.fasta -out GCF_003970675.1_ASM397067v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:30,167] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:30,170] [INFO] Selected 9 target genomes.
[2024-01-24 14:55:30,171] [INFO] Target genome list was writen to GCF_003970675.1_ASM397067v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:30,176] [INFO] Task started: fastANI
[2024-01-24 14:55:30,177] [INFO] Running command: fastANI --query /var/lib/cwl/stgd16ed542-af57-4dd7-9b3d-356f636ca660/GCF_003970675.1_ASM397067v1_genomic.fna.gz --refList GCF_003970675.1_ASM397067v1_genomic.fna/target_genomes.txt --output GCF_003970675.1_ASM397067v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:45,408] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:45,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63a36318-47ed-4478-ac36-5628501b35ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:45,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63a36318-47ed-4478-ac36-5628501b35ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:45,417] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:45,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:45,418] [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 pectinis	strain=L12M1	GCA_003970675.1	2494373	2494373	type	True	100.0	2225	2225	95	conclusive
Flammeovirga kamogawensis	strain=YS10	GCA_018736065.1	373891	373891	type	True	89.4555	1922	2225	95	below_threshold
Flammeovirga kamogawensis	strain=YS10	GCA_007097495.1	373891	373891	type	True	89.4507	1907	2225	95	below_threshold
Flammeovirga kamogawensis	strain=DSM 26273	GCA_014207545.1	373891	373891	type	True	89.3869	1870	2225	95	below_threshold
Flammeovirga yaeyamensis	strain=NBRC:100898	GCA_018736045.1	367791	367791	type	True	78.4249	533	2225	95	below_threshold
Flammeovirga aprica	strain=ATCC 23126	GCA_012844305.1	29528	29528	type	True	78.4139	585	2225	95	below_threshold
Flammeovirga agarivorans	strain=SR4	GCA_012641475.1	2726742	2726742	type	True	78.3619	626	2225	95	below_threshold
Flammeovirga pacifica	strain=WPAGA1	GCA_000807855.2	915059	915059	type	True	78.2956	627	2225	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:45,420] [INFO] DFAST Taxonomy check result was written to GCF_003970675.1_ASM397067v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:45,420] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:45,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:45,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63a36318-47ed-4478-ac36-5628501b35ce/dqc_reference/checkm_data
[2024-01-24 14:55:45,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:45,488] [INFO] Task started: CheckM
[2024-01-24 14:55:45,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970675.1_ASM397067v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970675.1_ASM397067v1_genomic.fna/checkm_input GCF_003970675.1_ASM397067v1_genomic.fna/checkm_result
[2024-01-24 14:56:41,397] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:41,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:41,433] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:41,433] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:41,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970675.1_ASM397067v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:41,434] [INFO] Task started: Blastn
[2024-01-24 14:56:41,435] [INFO] Running command: blastn -query GCF_003970675.1_ASM397067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63a36318-47ed-4478-ac36-5628501b35ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970675.1_ASM397067v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:42,229] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:42,234] [INFO] Selected 9 target genomes.
[2024-01-24 14:56:42,235] [INFO] Target genome list was writen to GCF_003970675.1_ASM397067v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:42,243] [INFO] Task started: fastANI
[2024-01-24 14:56:42,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgd16ed542-af57-4dd7-9b3d-356f636ca660/GCF_003970675.1_ASM397067v1_genomic.fna.gz --refList GCF_003970675.1_ASM397067v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970675.1_ASM397067v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:56,873] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:56,885] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:56,886] [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_003970675.1	s__Flammeovirga pectinis	100.0	2225	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018736065.1	s__Flammeovirga kamogawensis	89.435	1924	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	100.00	100.00	1.00	1.00	3	-
GCF_012844305.1	s__Flammeovirga aprica	78.3944	587	2225	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	78.3675	626	2225	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	78.3585	584	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018736045.1	s__Flammeovirga yaeyamensis	78.3304	531	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	98.83	96.49	0.96	0.89	4	-
GCF_000812565.1	s__Flammeovirga sp000812565	78.3008	602	2225	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	78.284	629	2225	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	78.2207	585	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:56,889] [INFO] GTDB search result was written to GCF_003970675.1_ASM397067v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:56,889] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:56,892] [INFO] DFAST_QC result json was written to GCF_003970675.1_ASM397067v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:56,892] [INFO] DFAST_QC completed!
[2024-01-24 14:56:56,892] [INFO] Total running time: 0h1m48s