[2024-01-24 13:01:38,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:38,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:38,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2683a20-5a50-4678-8341-f1f13990df5d/dqc_reference
[2024-01-24 13:01:40,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:40,904] [INFO] Task started: Prodigal
[2024-01-24 13:01:40,905] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f228680-cdb7-4456-a9a4-0be90d7abc2b/GCF_000835975.1_ASM83597v1_genomic.fna.gz | prodigal -d GCF_000835975.1_ASM83597v1_genomic.fna/cds.fna -a GCF_000835975.1_ASM83597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:45,981] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:45,981] [INFO] Task started: HMMsearch
[2024-01-24 13:01:45,981] [INFO] Running command: hmmsearch --tblout GCF_000835975.1_ASM83597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2683a20-5a50-4678-8341-f1f13990df5d/dqc_reference/reference_markers.hmm GCF_000835975.1_ASM83597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:46,275] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:46,276] [INFO] Found 6/6 markers.
[2024-01-24 13:01:46,309] [INFO] Query marker FASTA was written to GCF_000835975.1_ASM83597v1_genomic.fna/markers.fasta
[2024-01-24 13:01:46,310] [INFO] Task started: Blastn
[2024-01-24 13:01:46,311] [INFO] Running command: blastn -query GCF_000835975.1_ASM83597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2683a20-5a50-4678-8341-f1f13990df5d/dqc_reference/reference_markers.fasta -out GCF_000835975.1_ASM83597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:47,776] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:47,780] [INFO] Selected 10 target genomes.
[2024-01-24 13:01:47,781] [INFO] Target genome list was writen to GCF_000835975.1_ASM83597v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:47,791] [INFO] Task started: fastANI
[2024-01-24 13:01:47,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f228680-cdb7-4456-a9a4-0be90d7abc2b/GCF_000835975.1_ASM83597v1_genomic.fna.gz --refList GCF_000835975.1_ASM83597v1_genomic.fna/target_genomes.txt --output GCF_000835975.1_ASM83597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:53,179] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:53,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2683a20-5a50-4678-8341-f1f13990df5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:53,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2683a20-5a50-4678-8341-f1f13990df5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:53,189] [INFO] Found 10 fastANI hits (8 hits with ANI > threshold)
[2024-01-24 13:01:53,189] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:53,189] [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	strain=FDAARGOS_865	GCA_016028835.1	1358	1358	type	True	99.9892	815	817	95	conclusive
Lactococcus lactis subsp. lactis	strain=NBRC 100933	GCA_001514475.1	1360	1358	suspected-type	True	99.9864	816	817	95	conclusive
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_004354485.1	1360	1358	type	True	99.9735	802	817	95	conclusive
Lactococcus lactis	strain=ATCC 19435	GCA_900099625.1	1358	1358	type	True	99.9659	799	817	95	conclusive
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_001456385.1	1360	1358	type	True	99.9472	780	817	95	conclusive
Lactococcus lactis subsp. hordniae	strain=DSM 20450	GCA_002441785.1	203404	1358	type	True	97.1451	626	817	95	conclusive
Lactococcus lactis subsp. hordniae	strain=CCUG 32210T	GCA_008692945.1	203404	1358	type	True	97.1232	641	817	95	conclusive
Lactococcus lactis subsp. hordniae	strain=NBRC 100931	GCA_001591725.1	203404	1358	type	True	97.1115	631	817	95	conclusive
Lactococcus formosensis subsp. bovis	strain=LMG 30663	GCA_018403725.1	1850438	1281486	type	True	78.7816	122	817	95	below_threshold
Lactococcus paracarnosus	strain=TMW 2.1615	GCA_006770285.1	2749962	2749962	type	True	77.2802	62	817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:53,192] [INFO] DFAST Taxonomy check result was written to GCF_000835975.1_ASM83597v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:53,193] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:53,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:53,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2683a20-5a50-4678-8341-f1f13990df5d/dqc_reference/checkm_data
[2024-01-24 13:01:53,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:53,226] [INFO] Task started: CheckM
[2024-01-24 13:01:53,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000835975.1_ASM83597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000835975.1_ASM83597v1_genomic.fna/checkm_input GCF_000835975.1_ASM83597v1_genomic.fna/checkm_result
[2024-01-24 13:02:20,752] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:20,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:20,802] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:20,802] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:20,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000835975.1_ASM83597v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:20,803] [INFO] Task started: Blastn
[2024-01-24 13:02:20,804] [INFO] Running command: blastn -query GCF_000835975.1_ASM83597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2683a20-5a50-4678-8341-f1f13990df5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000835975.1_ASM83597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:21,705] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:21,709] [INFO] Selected 12 target genomes.
[2024-01-24 13:02:21,709] [INFO] Target genome list was writen to GCF_000835975.1_ASM83597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:21,719] [INFO] Task started: fastANI
[2024-01-24 13:02:21,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f228680-cdb7-4456-a9a4-0be90d7abc2b/GCF_000835975.1_ASM83597v1_genomic.fna.gz --refList GCF_000835975.1_ASM83597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000835975.1_ASM83597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:27,542] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:27,552] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:27,552] [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	99.9659	799	817	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	87.8782	571	817	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	84.5911	326	817	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	81.3768	365	817	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601015.1	s__Lactococcus hircilactis	80.0505	199	817	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	79.3235	296	817	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403765.1	s__Lactococcus nasutitermitis	79.3093	192	817	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	79.1429	318	817	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.72	98.72	0.90	0.90	2	-
GCF_018403745.1	s__Lactococcus formosensis	78.5917	135	817	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	78.2694	164	817	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	100.00	99.99	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:27,556] [INFO] GTDB search result was written to GCF_000835975.1_ASM83597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:27,557] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:27,560] [INFO] DFAST_QC result json was written to GCF_000835975.1_ASM83597v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:27,561] [INFO] DFAST_QC completed!
[2024-01-24 13:02:27,561] [INFO] Total running time: 0h0m49s