[2024-01-24 15:10:54,375] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:54,376] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:54,377] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbd20cf3-0bf8-4479-a9b7-cd9172901b53/dqc_reference
[2024-01-24 15:10:56,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,633] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,633] [INFO] Running command: gunzip -c /var/lib/cwl/stgd975e672-a31f-4655-b270-2c95eb5ea9ff/GCF_001591725.1_ASM159172v1_genomic.fna.gz | prodigal -d GCF_001591725.1_ASM159172v1_genomic.fna/cds.fna -a GCF_001591725.1_ASM159172v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:01,502] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:01,503] [INFO] Task started: HMMsearch
[2024-01-24 15:11:01,503] [INFO] Running command: hmmsearch --tblout GCF_001591725.1_ASM159172v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbd20cf3-0bf8-4479-a9b7-cd9172901b53/dqc_reference/reference_markers.hmm GCF_001591725.1_ASM159172v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:01,777] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:01,779] [INFO] Found 6/6 markers.
[2024-01-24 15:11:01,815] [INFO] Query marker FASTA was written to GCF_001591725.1_ASM159172v1_genomic.fna/markers.fasta
[2024-01-24 15:11:01,816] [INFO] Task started: Blastn
[2024-01-24 15:11:01,816] [INFO] Running command: blastn -query GCF_001591725.1_ASM159172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbd20cf3-0bf8-4479-a9b7-cd9172901b53/dqc_reference/reference_markers.fasta -out GCF_001591725.1_ASM159172v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:02,462] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:02,466] [INFO] Selected 7 target genomes.
[2024-01-24 15:11:02,466] [INFO] Target genome list was writen to GCF_001591725.1_ASM159172v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:02,473] [INFO] Task started: fastANI
[2024-01-24 15:11:02,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgd975e672-a31f-4655-b270-2c95eb5ea9ff/GCF_001591725.1_ASM159172v1_genomic.fna.gz --refList GCF_001591725.1_ASM159172v1_genomic.fna/target_genomes.txt --output GCF_001591725.1_ASM159172v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:06,275] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:06,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbd20cf3-0bf8-4479-a9b7-cd9172901b53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:06,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbd20cf3-0bf8-4479-a9b7-cd9172901b53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:06,283] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 15:11:06,284] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:06,284] [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 lactis subsp. hordniae	strain=NBRC 100931	GCA_001591725.1	203404	1358	type	True	100.0	771	774	95	conclusive
Lactococcus lactis subsp. hordniae	strain=CCUG 32210T	GCA_008692945.1	203404	1358	type	True	99.9899	769	774	95	conclusive
Lactococcus lactis subsp. hordniae	strain=DSM 20450	GCA_002441785.1	203404	1358	type	True	99.9724	755	774	95	conclusive
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_001456385.1	1360	1358	type	True	97.1715	630	774	95	conclusive
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_004354485.1	1360	1358	type	True	97.1186	644	774	95	conclusive
Lactococcus formosensis subsp. bovis	strain=LMG 30663	GCA_018403725.1	1850438	1281486	type	True	78.3242	133	774	95	below_threshold
Lactococcus paracarnosus	strain=TMW 2.1615	GCA_006770285.1	2749962	2749962	type	True	77.0804	57	774	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:06,285] [INFO] DFAST Taxonomy check result was written to GCF_001591725.1_ASM159172v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:06,286] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:06,286] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:06,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbd20cf3-0bf8-4479-a9b7-cd9172901b53/dqc_reference/checkm_data
[2024-01-24 15:11:06,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:06,318] [INFO] Task started: CheckM
[2024-01-24 15:11:06,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591725.1_ASM159172v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591725.1_ASM159172v1_genomic.fna/checkm_input GCF_001591725.1_ASM159172v1_genomic.fna/checkm_result
[2024-01-24 15:11:30,176] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:30,177] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:30,194] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:30,194] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:30,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591725.1_ASM159172v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:30,195] [INFO] Task started: Blastn
[2024-01-24 15:11:30,196] [INFO] Running command: blastn -query GCF_001591725.1_ASM159172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbd20cf3-0bf8-4479-a9b7-cd9172901b53/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591725.1_ASM159172v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:31,084] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:31,087] [INFO] Selected 13 target genomes.
[2024-01-24 15:11:31,087] [INFO] Target genome list was writen to GCF_001591725.1_ASM159172v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:31,098] [INFO] Task started: fastANI
[2024-01-24 15:11:31,099] [INFO] Running command: fastANI --query /var/lib/cwl/stgd975e672-a31f-4655-b270-2c95eb5ea9ff/GCF_001591725.1_ASM159172v1_genomic.fna.gz --refList GCF_001591725.1_ASM159172v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591725.1_ASM159172v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:37,122] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:37,133] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:37,133] [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_900099625.1	s__Lactococcus lactis	97.198	637	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.37	97.03	0.87	0.82	223	conclusive
GCF_001591705.1	s__Lactococcus cremoris	87.3958	542	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.76	97.45	0.91	0.82	70	-
GCF_014905395.1	s__Lactococcus taiwanensis	84.4227	331	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.39	0.94	0.93	6	-
GCF_004210295.1	s__Lactococcus sp004210295	81.267	347	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006965445.1	s__Lactococcus sp006965445	79.1753	302	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.72	98.72	0.90	0.90	2	-
GCF_009601015.1	s__Lactococcus hircilactis	79.1529	154	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627095.1	s__Lactococcus allomyrinae	79.1108	304	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403745.1	s__Lactococcus formosensis	78.5095	136	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.20	97.52	0.88	0.85	8	-
GCF_009601055.1	s__Lactococcus sp009601055	78.4338	147	774	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	77.8873	172	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101445.1	s__Streptococcus equinus_B	77.805	57	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_000154985.1	s__Streptococcus infantarius	77.4365	62	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:37,136] [INFO] GTDB search result was written to GCF_001591725.1_ASM159172v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:37,137] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:37,142] [INFO] DFAST_QC result json was written to GCF_001591725.1_ASM159172v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:37,142] [INFO] DFAST_QC completed!
[2024-01-24 15:11:37,143] [INFO] Total running time: 0h0m43s