[2024-01-24 14:30:47,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:47,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:47,173] [INFO] DQC Reference Directory: /var/lib/cwl/stge639b793-eb4c-4677-91e8-6feb3d6c0387/dqc_reference
[2024-01-24 14:30:48,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,395] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,395] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b8def1a-abd7-4630-bcfe-a12d61b653e6/GCF_009601015.1_ASM960101v1_genomic.fna.gz | prodigal -d GCF_009601015.1_ASM960101v1_genomic.fna/cds.fna -a GCF_009601015.1_ASM960101v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:54,269] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:54,269] [INFO] Task started: HMMsearch
[2024-01-24 14:30:54,270] [INFO] Running command: hmmsearch --tblout GCF_009601015.1_ASM960101v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge639b793-eb4c-4677-91e8-6feb3d6c0387/dqc_reference/reference_markers.hmm GCF_009601015.1_ASM960101v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:54,549] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:54,551] [INFO] Found 6/6 markers.
[2024-01-24 14:30:54,581] [INFO] Query marker FASTA was written to GCF_009601015.1_ASM960101v1_genomic.fna/markers.fasta
[2024-01-24 14:30:54,581] [INFO] Task started: Blastn
[2024-01-24 14:30:54,582] [INFO] Running command: blastn -query GCF_009601015.1_ASM960101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge639b793-eb4c-4677-91e8-6feb3d6c0387/dqc_reference/reference_markers.fasta -out GCF_009601015.1_ASM960101v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:55,166] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:55,169] [INFO] Selected 24 target genomes.
[2024-01-24 14:30:55,170] [INFO] Target genome list was writen to GCF_009601015.1_ASM960101v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:55,192] [INFO] Task started: fastANI
[2024-01-24 14:30:55,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b8def1a-abd7-4630-bcfe-a12d61b653e6/GCF_009601015.1_ASM960101v1_genomic.fna.gz --refList GCF_009601015.1_ASM960101v1_genomic.fna/target_genomes.txt --output GCF_009601015.1_ASM960101v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:06,377] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:06,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge639b793-eb4c-4677-91e8-6feb3d6c0387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:06,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge639b793-eb4c-4677-91e8-6feb3d6c0387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:06,390] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:06,390] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:06,390] [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
Lactococcus hircilactis	strain=DSM 28960	GCA_009601015.1	1494462	1494462	type	True	100.0	828	830	95	conclusive
Lactococcus lactis	strain=ATCC 19435	GCA_900099625.1	1358	1358	type	True	79.9191	202	830	95	below_threshold
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_001456385.1	1360	1358	type	True	79.7878	201	830	95	below_threshold
Lactococcus nasutitermitis	strain=NBRC 111537	GCA_018403765.1	1652957	1652957	type	True	79.7312	194	830	95	below_threshold
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_004354485.1	1360	1358	type	True	79.728	206	830	95	below_threshold
Lactococcus fujiensis	strain=JCM 16395	GCA_001311235.1	610251	610251	type	True	78.9695	210	830	95	below_threshold
Lactococcus fujiensis	strain=JCM 16395	GCA_002441655.1	610251	610251	type	True	78.7891	215	830	95	below_threshold
Lactococcus lactis subsp. hordniae	strain=DSM 20450	GCA_002441785.1	203404	1358	type	True	78.7658	163	830	95	below_threshold
Lactococcus taiwanensis	strain=NBRC 109049	GCA_014905395.1	1151742	1151742	type	True	78.0514	134	830	95	below_threshold
Lactococcus allomyrinae	strain=1JSPR-7	GCA_003627095.1	2419773	2419773	type	True	77.5841	166	830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:06,392] [INFO] DFAST Taxonomy check result was written to GCF_009601015.1_ASM960101v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:06,392] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:06,392] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:06,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge639b793-eb4c-4677-91e8-6feb3d6c0387/dqc_reference/checkm_data
[2024-01-24 14:31:06,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:06,420] [INFO] Task started: CheckM
[2024-01-24 14:31:06,420] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009601015.1_ASM960101v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009601015.1_ASM960101v1_genomic.fna/checkm_input GCF_009601015.1_ASM960101v1_genomic.fna/checkm_result
[2024-01-24 14:31:33,267] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:33,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:33,288] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:33,288] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:33,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009601015.1_ASM960101v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:33,289] [INFO] Task started: Blastn
[2024-01-24 14:31:33,290] [INFO] Running command: blastn -query GCF_009601015.1_ASM960101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge639b793-eb4c-4677-91e8-6feb3d6c0387/dqc_reference/reference_markers_gtdb.fasta -out GCF_009601015.1_ASM960101v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:34,123] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:34,126] [INFO] Selected 22 target genomes.
[2024-01-24 14:31:34,126] [INFO] Target genome list was writen to GCF_009601015.1_ASM960101v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:34,143] [INFO] Task started: fastANI
[2024-01-24 14:31:34,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b8def1a-abd7-4630-bcfe-a12d61b653e6/GCF_009601015.1_ASM960101v1_genomic.fna.gz --refList GCF_009601015.1_ASM960101v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009601015.1_ASM960101v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:43,056] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:43,065] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:43,065] [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_009601015.1	s__Lactococcus hircilactis	100.0	828	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900099625.1	s__Lactococcus lactis	79.866	204	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.37	97.03	0.87	0.82	223	-
GCF_001591705.1	s__Lactococcus cremoris	79.781	171	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.76	97.45	0.91	0.82	70	-
GCF_018403765.1	s__Lactococcus nasutitermitis	79.7312	194	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601055.1	s__Lactococcus sp009601055	78.8709	251	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	100.00	99.99	0.99	0.98	3	-
GCF_002441655.1	s__Lactococcus fujiensis	78.7891	215	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	99.84	99.84	0.99	0.99	2	-
GCF_016027715.1	s__Lactococcus garvieae_A	78.768	88	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.50	0.90	0.89	3	-
GCF_014905395.1	s__Lactococcus taiwanensis	78.0514	134	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.39	0.94	0.93	6	-
GCF_003627095.1	s__Lactococcus allomyrinae	77.5395	167	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:43,070] [INFO] GTDB search result was written to GCF_009601015.1_ASM960101v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:43,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:43,076] [INFO] DFAST_QC result json was written to GCF_009601015.1_ASM960101v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:43,076] [INFO] DFAST_QC completed!
[2024-01-24 14:31:43,077] [INFO] Total running time: 0h0m56s