[2024-01-24 11:58:56,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:56,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:56,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg58a2a729-ba8c-4804-8745-18a17f94bd3e/dqc_reference
[2024-01-24 11:58:58,132] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,133] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,133] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d9c27a8-eaa6-4ed1-a16b-52d74b0c5506/GCF_000807855.2_ASM80785v2_genomic.fna.gz | prodigal -d GCF_000807855.2_ASM80785v2_genomic.fna/cds.fna -a GCF_000807855.2_ASM80785v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:18,662] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:18,662] [INFO] Task started: HMMsearch
[2024-01-24 11:59:18,662] [INFO] Running command: hmmsearch --tblout GCF_000807855.2_ASM80785v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58a2a729-ba8c-4804-8745-18a17f94bd3e/dqc_reference/reference_markers.hmm GCF_000807855.2_ASM80785v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:19,043] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:19,044] [INFO] Found 6/6 markers.
[2024-01-24 11:59:19,127] [INFO] Query marker FASTA was written to GCF_000807855.2_ASM80785v2_genomic.fna/markers.fasta
[2024-01-24 11:59:19,127] [INFO] Task started: Blastn
[2024-01-24 11:59:19,127] [INFO] Running command: blastn -query GCF_000807855.2_ASM80785v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg58a2a729-ba8c-4804-8745-18a17f94bd3e/dqc_reference/reference_markers.fasta -out GCF_000807855.2_ASM80785v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:19,761] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:19,765] [INFO] Selected 11 target genomes.
[2024-01-24 11:59:19,765] [INFO] Target genome list was writen to GCF_000807855.2_ASM80785v2_genomic.fna/target_genomes.txt
[2024-01-24 11:59:19,769] [INFO] Task started: fastANI
[2024-01-24 11:59:19,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d9c27a8-eaa6-4ed1-a16b-52d74b0c5506/GCF_000807855.2_ASM80785v2_genomic.fna.gz --refList GCF_000807855.2_ASM80785v2_genomic.fna/target_genomes.txt --output GCF_000807855.2_ASM80785v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:31,171] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:31,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58a2a729-ba8c-4804-8745-18a17f94bd3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:31,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58a2a729-ba8c-4804-8745-18a17f94bd3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:31,178] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:31,178] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:31,178] [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 pacifica	strain=WPAGA1	GCA_000807855.2	915059	915059	type	True	99.9848	2177	2195	95	conclusive
Flammeovirga yaeyamensis	strain=NBRC:100898	GCA_018736045.1	367791	367791	type	True	81.5301	1293	2195	95	below_threshold
Flammeovirga yaeyamensis	strain=DSM 25626	GCA_014195575.1	367791	367791	type	True	81.5173	1284	2195	95	below_threshold
Flammeovirga yaeyamensis	strain=NBRC 100898	GCA_012844325.1	367791	367791	type	True	81.4902	1286	2195	95	below_threshold
Flammeovirga agarivorans	strain=SR4	GCA_012641475.1	2726742	2726742	type	True	78.9005	728	2195	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	75.5223	50	2195	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:31,179] [INFO] DFAST Taxonomy check result was written to GCF_000807855.2_ASM80785v2_genomic.fna/tc_result.tsv
[2024-01-24 11:59:31,181] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:31,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:31,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58a2a729-ba8c-4804-8745-18a17f94bd3e/dqc_reference/checkm_data
[2024-01-24 11:59:31,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:31,247] [INFO] Task started: CheckM
[2024-01-24 11:59:31,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000807855.2_ASM80785v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000807855.2_ASM80785v2_genomic.fna/checkm_input GCF_000807855.2_ASM80785v2_genomic.fna/checkm_result
[2024-01-24 12:00:30,278] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:30,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:30,300] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:30,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:30,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000807855.2_ASM80785v2_genomic.fna/markers.fasta)
[2024-01-24 12:00:30,301] [INFO] Task started: Blastn
[2024-01-24 12:00:30,301] [INFO] Running command: blastn -query GCF_000807855.2_ASM80785v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg58a2a729-ba8c-4804-8745-18a17f94bd3e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000807855.2_ASM80785v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:31,073] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:31,076] [INFO] Selected 13 target genomes.
[2024-01-24 12:00:31,076] [INFO] Target genome list was writen to GCF_000807855.2_ASM80785v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:31,107] [INFO] Task started: fastANI
[2024-01-24 12:00:31,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d9c27a8-eaa6-4ed1-a16b-52d74b0c5506/GCF_000807855.2_ASM80785v2_genomic.fna.gz --refList GCF_000807855.2_ASM80785v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000807855.2_ASM80785v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:46,447] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:46,456] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:46,456] [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_000807855.2	s__Flammeovirga pacifica	99.9848	2177	2195	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_018736045.1	s__Flammeovirga yaeyamensis	81.5496	1291	2195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	98.83	96.49	0.96	0.89	4	-
GCF_012641475.1	s__Flammeovirga sp012641475	78.9019	727	2195	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	78.5106	603	2195	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	78.4825	599	2195	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	78.4677	607	2195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018736065.1	s__Flammeovirga kamogawensis	78.3791	625	2195	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	78.3297	592	2195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970675.1	s__Flammeovirga pectinis	78.3107	641	2195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004762155.1	s__Tenacibaculum sp004762155	75.1785	70	2195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365575.1	s__Hypnocyclicus thermotrophus	74.9641	57	2195	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Hypnocyclicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:46,458] [INFO] GTDB search result was written to GCF_000807855.2_ASM80785v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:46,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:46,461] [INFO] DFAST_QC result json was written to GCF_000807855.2_ASM80785v2_genomic.fna/dqc_result.json
[2024-01-24 12:00:46,461] [INFO] DFAST_QC completed!
[2024-01-24 12:00:46,461] [INFO] Total running time: 0h1m50s