[2024-01-24 13:40:28,729] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg9448b33b-c45b-4336-aeab-31e3d6f07c9f/dqc_reference
[2024-01-24 13:40:31,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,145] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,145] [INFO] Running command: gunzip -c /var/lib/cwl/stga03abbd2-2409-438c-9a63-a8a169817503/GCF_006965445.1_ASM696544v1_genomic.fna.gz | prodigal -d GCF_006965445.1_ASM696544v1_genomic.fna/cds.fna -a GCF_006965445.1_ASM696544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:37,244] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:37,244] [INFO] Task started: HMMsearch
[2024-01-24 13:40:37,244] [INFO] Running command: hmmsearch --tblout GCF_006965445.1_ASM696544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9448b33b-c45b-4336-aeab-31e3d6f07c9f/dqc_reference/reference_markers.hmm GCF_006965445.1_ASM696544v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:37,562] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:37,564] [INFO] Found 6/6 markers.
[2024-01-24 13:40:37,607] [INFO] Query marker FASTA was written to GCF_006965445.1_ASM696544v1_genomic.fna/markers.fasta
[2024-01-24 13:40:37,607] [INFO] Task started: Blastn
[2024-01-24 13:40:37,608] [INFO] Running command: blastn -query GCF_006965445.1_ASM696544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9448b33b-c45b-4336-aeab-31e3d6f07c9f/dqc_reference/reference_markers.fasta -out GCF_006965445.1_ASM696544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:38,310] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:38,313] [INFO] Selected 19 target genomes.
[2024-01-24 13:40:38,314] [INFO] Target genome list was writen to GCF_006965445.1_ASM696544v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:38,323] [INFO] Task started: fastANI
[2024-01-24 13:40:38,323] [INFO] Running command: fastANI --query /var/lib/cwl/stga03abbd2-2409-438c-9a63-a8a169817503/GCF_006965445.1_ASM696544v1_genomic.fna.gz --refList GCF_006965445.1_ASM696544v1_genomic.fna/target_genomes.txt --output GCF_006965445.1_ASM696544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:52,960] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:52,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9448b33b-c45b-4336-aeab-31e3d6f07c9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:52,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9448b33b-c45b-4336-aeab-31e3d6f07c9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:52,972] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:52,973] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:52,973] [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 protaetiae	strain=KACC 19320	GCA_006965445.1	2592653	2592653	type	True	100.0	897	898	95	conclusive
Lactococcus allomyrinae	strain=1JSPR-7	GCA_003627095.1	2419773	2419773	type	True	93.534	775	898	95	below_threshold
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_004354485.1	1360	1358	type	True	79.505	318	898	95	below_threshold
Lactococcus lactis subsp. hordniae	strain=DSM 20450	GCA_002441785.1	203404	1358	type	True	79.259	295	898	95	below_threshold
Lactococcus lactis	strain=ATCC 19435	GCA_900099625.1	1358	1358	type	True	79.1337	312	898	95	below_threshold
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_001456385.1	1360	1358	type	True	79.0751	310	898	95	below_threshold
Lactococcus taiwanensis	strain=NBRC 109049	GCA_014905395.1	1151742	1151742	type	True	79.031	239	898	95	below_threshold
Lactococcus fujiensis	strain=JCM 16395	GCA_001311235.1	610251	610251	type	True	78.0116	122	898	95	below_threshold
Lactococcus fujiensis	strain=JCM 16395	GCA_002441655.1	610251	610251	type	True	77.9109	123	898	95	below_threshold
Lactococcus nasutitermitis	strain=NBRC 111537	GCA_018403765.1	1652957	1652957	type	True	77.8369	176	898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:52,975] [INFO] DFAST Taxonomy check result was written to GCF_006965445.1_ASM696544v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:52,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:52,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:52,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9448b33b-c45b-4336-aeab-31e3d6f07c9f/dqc_reference/checkm_data
[2024-01-24 13:40:52,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:53,011] [INFO] Task started: CheckM
[2024-01-24 13:40:53,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006965445.1_ASM696544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006965445.1_ASM696544v1_genomic.fna/checkm_input GCF_006965445.1_ASM696544v1_genomic.fna/checkm_result
[2024-01-24 13:41:19,268] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:19,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:19,295] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:19,295] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:19,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006965445.1_ASM696544v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:19,296] [INFO] Task started: Blastn
[2024-01-24 13:41:19,296] [INFO] Running command: blastn -query GCF_006965445.1_ASM696544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9448b33b-c45b-4336-aeab-31e3d6f07c9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_006965445.1_ASM696544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:20,112] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:20,117] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:20,117] [INFO] Target genome list was writen to GCF_006965445.1_ASM696544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:20,156] [INFO] Task started: fastANI
[2024-01-24 13:41:20,156] [INFO] Running command: fastANI --query /var/lib/cwl/stga03abbd2-2409-438c-9a63-a8a169817503/GCF_006965445.1_ASM696544v1_genomic.fna.gz --refList GCF_006965445.1_ASM696544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006965445.1_ASM696544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:32,849] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:32,863] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:32,863] [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_006965445.1	s__Lactococcus sp006965445	100.0	896	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.72	98.72	0.90	0.90	2	conclusive
GCF_003627095.1	s__Lactococcus allomyrinae	93.5516	776	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004210295.1	s__Lactococcus sp004210295	79.7132	263	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099625.1	s__Lactococcus lactis	79.1192	313	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.37	97.03	0.87	0.82	223	-
GCF_014905395.1	s__Lactococcus taiwanensis	79.0578	240	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.39	0.94	0.93	6	-
GCF_900475675.1	s__Streptococcus lutetiensis	79.0481	55	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_001591705.1	s__Lactococcus cremoris	79.0095	287	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.76	97.45	0.91	0.82	70	-
GCF_002441655.1	s__Lactococcus fujiensis	77.9387	122	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	99.84	99.84	0.99	0.99	2	-
GCF_009601055.1	s__Lactococcus sp009601055	77.8509	157	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	100.00	99.99	0.99	0.98	3	-
GCF_018403765.1	s__Lactococcus nasutitermitis	77.8369	176	898	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 13:41:32,871] [INFO] GTDB search result was written to GCF_006965445.1_ASM696544v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:32,871] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:32,875] [INFO] DFAST_QC result json was written to GCF_006965445.1_ASM696544v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:32,875] [INFO] DFAST_QC completed!
[2024-01-24 13:41:32,875] [INFO] Total running time: 0h1m4s