[2024-01-24 11:43:36,409] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:36,412] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:36,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c5cd8cc-9851-48ba-9299-4d39f81f6527/dqc_reference
[2024-01-24 11:43:37,702] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:37,703] [INFO] Task started: Prodigal
[2024-01-24 11:43:37,703] [INFO] Running command: gunzip -c /var/lib/cwl/stg20b487b6-94fc-4cb8-93c7-77ccfdd7b09a/GCF_003001855.1_ASM300185v1_genomic.fna.gz | prodigal -d GCF_003001855.1_ASM300185v1_genomic.fna/cds.fna -a GCF_003001855.1_ASM300185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:47,751] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:47,751] [INFO] Task started: HMMsearch
[2024-01-24 11:43:47,751] [INFO] Running command: hmmsearch --tblout GCF_003001855.1_ASM300185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c5cd8cc-9851-48ba-9299-4d39f81f6527/dqc_reference/reference_markers.hmm GCF_003001855.1_ASM300185v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:48,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:48,123] [INFO] Found 6/6 markers.
[2024-01-24 11:43:48,154] [INFO] Query marker FASTA was written to GCF_003001855.1_ASM300185v1_genomic.fna/markers.fasta
[2024-01-24 11:43:48,154] [INFO] Task started: Blastn
[2024-01-24 11:43:48,154] [INFO] Running command: blastn -query GCF_003001855.1_ASM300185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c5cd8cc-9851-48ba-9299-4d39f81f6527/dqc_reference/reference_markers.fasta -out GCF_003001855.1_ASM300185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:48,858] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:48,862] [INFO] Selected 12 target genomes.
[2024-01-24 11:43:48,863] [INFO] Target genome list was writen to GCF_003001855.1_ASM300185v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:48,902] [INFO] Task started: fastANI
[2024-01-24 11:43:48,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg20b487b6-94fc-4cb8-93c7-77ccfdd7b09a/GCF_003001855.1_ASM300185v1_genomic.fna.gz --refList GCF_003001855.1_ASM300185v1_genomic.fna/target_genomes.txt --output GCF_003001855.1_ASM300185v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:56,836] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:56,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c5cd8cc-9851-48ba-9299-4d39f81f6527/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:56,837] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c5cd8cc-9851-48ba-9299-4d39f81f6527/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:56,846] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:43:56,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:56,847] [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
Nonlabens ulvanivorans	strain=DSM 22727	GCA_003001855.1	906888	906888	type	True	100.0	1045	1045	95	conclusive
Nonlabens ulvanivorans	strain=PLR	GCA_000732625.1	906888	906888	type	True	99.9826	1037	1045	95	conclusive
Nonlabens arenilitoris	strain=KCTC 32109	GCA_002954765.1	1217969	1217969	type	True	89.0566	912	1045	95	below_threshold
Nonlabens xylanidelens	strain=DSM 16809	GCA_002934445.1	191564	191564	type	True	79.5464	388	1045	95	below_threshold
Nonlabens xylanidelens	strain=DSM 16809	GCA_002954345.1	191564	191564	type	True	79.5058	395	1045	95	below_threshold
Nonlabens dokdonensis	strain=DSW-6	GCA_000332115.1	328515	328515	type	True	78.8563	351	1045	95	below_threshold
Nonlabens dokdonensis	strain=DSM 17205	GCA_003254015.1	328515	328515	type	True	78.8362	348	1045	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.6967	84	1045	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.5089	51	1045	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.4639	77	1045	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.3612	75	1045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:56,854] [INFO] DFAST Taxonomy check result was written to GCF_003001855.1_ASM300185v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:56,855] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:56,855] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:56,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c5cd8cc-9851-48ba-9299-4d39f81f6527/dqc_reference/checkm_data
[2024-01-24 11:43:56,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:56,895] [INFO] Task started: CheckM
[2024-01-24 11:43:56,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003001855.1_ASM300185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003001855.1_ASM300185v1_genomic.fna/checkm_input GCF_003001855.1_ASM300185v1_genomic.fna/checkm_result
[2024-01-24 11:44:32,728] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:32,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:32,750] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:32,751] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:32,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003001855.1_ASM300185v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:32,751] [INFO] Task started: Blastn
[2024-01-24 11:44:32,751] [INFO] Running command: blastn -query GCF_003001855.1_ASM300185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c5cd8cc-9851-48ba-9299-4d39f81f6527/dqc_reference/reference_markers_gtdb.fasta -out GCF_003001855.1_ASM300185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:33,590] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:33,594] [INFO] Selected 7 target genomes.
[2024-01-24 11:44:33,594] [INFO] Target genome list was writen to GCF_003001855.1_ASM300185v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:33,625] [INFO] Task started: fastANI
[2024-01-24 11:44:33,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg20b487b6-94fc-4cb8-93c7-77ccfdd7b09a/GCF_003001855.1_ASM300185v1_genomic.fna.gz --refList GCF_003001855.1_ASM300185v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003001855.1_ASM300185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:39,069] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:39,083] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:39,083] [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_000732625.1	s__Nonlabens ulvanivorans	99.9826	1037	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	98.59	98.07	0.92	0.89	5	conclusive
GCF_000755285.1	s__Nonlabens ulvanivorans_A	91.2222	911	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	97.55	97.55	0.94	0.94	2	-
GCF_002954765.1	s__Nonlabens arenilitoris	89.0501	913	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153385.1	s__Nonlabens sp000153385	88.3389	904	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934445.1	s__Nonlabens xylanidelens	79.5339	389	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002162835.1	s__Nonlabens dokdonensis_B	78.8909	309	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332115.1	s__Nonlabens dokdonensis	78.8559	351	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:39,085] [INFO] GTDB search result was written to GCF_003001855.1_ASM300185v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:39,085] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:39,088] [INFO] DFAST_QC result json was written to GCF_003001855.1_ASM300185v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:39,089] [INFO] DFAST_QC completed!
[2024-01-24 11:44:39,089] [INFO] Total running time: 0h1m3s