[2024-01-24 15:02:36,475] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:36,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:36,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg15396a32-f395-4ac4-a0c6-1d070746f981/dqc_reference
[2024-01-24 15:02:38,276] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,278] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,279] [INFO] Running command: gunzip -c /var/lib/cwl/stg0da759da-bbc0-47bf-9a3f-f0990e62af34/GCF_014207545.1_ASM1420754v1_genomic.fna.gz | prodigal -d GCF_014207545.1_ASM1420754v1_genomic.fna/cds.fna -a GCF_014207545.1_ASM1420754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:58,639] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:58,640] [INFO] Task started: HMMsearch
[2024-01-24 15:02:58,640] [INFO] Running command: hmmsearch --tblout GCF_014207545.1_ASM1420754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15396a32-f395-4ac4-a0c6-1d070746f981/dqc_reference/reference_markers.hmm GCF_014207545.1_ASM1420754v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:59,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:59,052] [INFO] Found 6/6 markers.
[2024-01-24 15:02:59,124] [INFO] Query marker FASTA was written to GCF_014207545.1_ASM1420754v1_genomic.fna/markers.fasta
[2024-01-24 15:02:59,124] [INFO] Task started: Blastn
[2024-01-24 15:02:59,125] [INFO] Running command: blastn -query GCF_014207545.1_ASM1420754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15396a32-f395-4ac4-a0c6-1d070746f981/dqc_reference/reference_markers.fasta -out GCF_014207545.1_ASM1420754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:59,804] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:59,808] [INFO] Selected 9 target genomes.
[2024-01-24 15:02:59,808] [INFO] Target genome list was writen to GCF_014207545.1_ASM1420754v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:59,823] [INFO] Task started: fastANI
[2024-01-24 15:02:59,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg0da759da-bbc0-47bf-9a3f-f0990e62af34/GCF_014207545.1_ASM1420754v1_genomic.fna.gz --refList GCF_014207545.1_ASM1420754v1_genomic.fna/target_genomes.txt --output GCF_014207545.1_ASM1420754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:11,863] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:11,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15396a32-f395-4ac4-a0c6-1d070746f981/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:11,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15396a32-f395-4ac4-a0c6-1d070746f981/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:11,872] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:03:11,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:11,872] [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=DSM 26273	GCA_014207545.1	373891	373891	type	True	100.0	2255	2257	95	conclusive
Flammeovirga kamogawensis	strain=YS10	GCA_007097495.1	373891	373891	type	True	99.9977	2254	2257	95	conclusive
Flammeovirga kamogawensis	strain=YS10	GCA_018736065.1	373891	373891	type	True	99.9911	2256	2257	95	conclusive
Flammeovirga pectinis	strain=L12M1	GCA_003970675.1	2494373	2494373	type	True	89.3251	1887	2257	95	below_threshold
Flammeovirga aprica	strain=ATCC 23126	GCA_012844305.1	29528	29528	type	True	78.4676	590	2257	95	below_threshold
Flammeovirga pacifica	strain=WPAGA1	GCA_000807855.2	915059	915059	type	True	78.2876	611	2257	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	75.3748	55	2257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:11,874] [INFO] DFAST Taxonomy check result was written to GCF_014207545.1_ASM1420754v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:11,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:11,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:11,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15396a32-f395-4ac4-a0c6-1d070746f981/dqc_reference/checkm_data
[2024-01-24 15:03:11,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:11,945] [INFO] Task started: CheckM
[2024-01-24 15:03:11,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207545.1_ASM1420754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207545.1_ASM1420754v1_genomic.fna/checkm_input GCF_014207545.1_ASM1420754v1_genomic.fna/checkm_result
[2024-01-24 15:04:11,013] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:11,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:11,044] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:11,044] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:11,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207545.1_ASM1420754v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:11,045] [INFO] Task started: Blastn
[2024-01-24 15:04:11,045] [INFO] Running command: blastn -query GCF_014207545.1_ASM1420754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15396a32-f395-4ac4-a0c6-1d070746f981/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207545.1_ASM1420754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:11,916] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:11,920] [INFO] Selected 12 target genomes.
[2024-01-24 15:04:11,920] [INFO] Target genome list was writen to GCF_014207545.1_ASM1420754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:11,933] [INFO] Task started: fastANI
[2024-01-24 15:04:11,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg0da759da-bbc0-47bf-9a3f-f0990e62af34/GCF_014207545.1_ASM1420754v1_genomic.fna.gz --refList GCF_014207545.1_ASM1420754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207545.1_ASM1420754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:27,400] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:27,410] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:27,410] [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	99.9911	2256	2257	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	89.3385	1885	2257	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	78.4711	589	2257	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	78.4251	590	2257	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	78.3917	609	2257	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	78.3903	668	2257	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	78.3845	631	2257	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	78.3011	608	2257	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	75.3748	55	2257	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	74.9203	52	2257	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 15:04:27,417] [INFO] GTDB search result was written to GCF_014207545.1_ASM1420754v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:27,418] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:27,421] [INFO] DFAST_QC result json was written to GCF_014207545.1_ASM1420754v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:27,421] [INFO] DFAST_QC completed!
[2024-01-24 15:04:27,421] [INFO] Total running time: 0h1m51s