[2024-01-25 19:36:20,755] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:20,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:20,757] [INFO] DQC Reference Directory: /var/lib/cwl/stgb68c4f6a-b156-47fc-981f-aa9d1674fe68/dqc_reference
[2024-01-25 19:36:21,892] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:21,893] [INFO] Task started: Prodigal
[2024-01-25 19:36:21,893] [INFO] Running command: gunzip -c /var/lib/cwl/stg1edac0e7-c015-4408-9cbe-909f738db45b/GCF_014905395.1_ASM1490539v1_genomic.fna.gz | prodigal -d GCF_014905395.1_ASM1490539v1_genomic.fna/cds.fna -a GCF_014905395.1_ASM1490539v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:25,703] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:25,703] [INFO] Task started: HMMsearch
[2024-01-25 19:36:25,704] [INFO] Running command: hmmsearch --tblout GCF_014905395.1_ASM1490539v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb68c4f6a-b156-47fc-981f-aa9d1674fe68/dqc_reference/reference_markers.hmm GCF_014905395.1_ASM1490539v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:25,913] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:25,914] [INFO] Found 6/6 markers.
[2024-01-25 19:36:25,932] [INFO] Query marker FASTA was written to GCF_014905395.1_ASM1490539v1_genomic.fna/markers.fasta
[2024-01-25 19:36:25,933] [INFO] Task started: Blastn
[2024-01-25 19:36:25,933] [INFO] Running command: blastn -query GCF_014905395.1_ASM1490539v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb68c4f6a-b156-47fc-981f-aa9d1674fe68/dqc_reference/reference_markers.fasta -out GCF_014905395.1_ASM1490539v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:26,482] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:26,484] [INFO] Selected 19 target genomes.
[2024-01-25 19:36:26,485] [INFO] Target genome list was writen to GCF_014905395.1_ASM1490539v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:26,492] [INFO] Task started: fastANI
[2024-01-25 19:36:26,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg1edac0e7-c015-4408-9cbe-909f738db45b/GCF_014905395.1_ASM1490539v1_genomic.fna.gz --refList GCF_014905395.1_ASM1490539v1_genomic.fna/target_genomes.txt --output GCF_014905395.1_ASM1490539v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:34,040] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:34,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb68c4f6a-b156-47fc-981f-aa9d1674fe68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:34,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb68c4f6a-b156-47fc-981f-aa9d1674fe68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:34,051] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:36:34,051] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:34,051] [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 taiwanensis	strain=NBRC 109049	GCA_014905395.1	1151742	1151742	type	True	100.0	644	645	95	conclusive
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_004354485.1	1360	1358	type	True	84.6302	328	645	95	below_threshold
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_001456385.1	1360	1358	type	True	84.6226	330	645	95	below_threshold
Lactococcus lactis subsp. lactis	strain=NBRC 100933	GCA_001514475.1	1360	1358	suspected-type	True	84.6042	328	645	95	below_threshold
Lactococcus lactis	strain=ATCC 19435	GCA_900099625.1	1358	1358	type	True	84.534	327	645	95	below_threshold
Lactococcus lactis subsp. hordniae	strain=DSM 20450	GCA_002441785.1	203404	1358	type	True	84.1704	324	645	95	below_threshold
Lactococcus lactis subsp. hordniae	strain=CCUG 32210T	GCA_008692945.1	203404	1358	type	True	84.1633	328	645	95	below_threshold
Lactococcus lactis subsp. hordniae	strain=NBRC 100931	GCA_001591725.1	203404	1358	type	True	84.1238	332	645	95	below_threshold
Lactococcus cremoris	strain=ATCC 19257	GCA_004354515.1	1359	1359	type	True	82.0522	308	645	95	below_threshold
Lactococcus cremoris subsp. cremoris	strain=NBRC 100676	GCA_001591705.1	2816960	1359	type	True	81.9758	310	645	95	below_threshold
Lactococcus cremoris	strain=LMG6897	GCA_001622295.1	1359	1359	type	True	81.9409	300	645	95	below_threshold
Lactococcus cremoris	strain=ATCC 19257	GCA_002441765.1	1359	1359	type	True	81.8934	293	645	95	below_threshold
Lactococcus allomyrinae	strain=1JSPR-7	GCA_003627095.1	2419773	2419773	type	True	79.2932	218	645	95	below_threshold
Lactococcus protaetiae	strain=KACC 19320	GCA_006965445.1	2592653	2592653	type	True	79.0974	234	645	95	below_threshold
Lactococcus formosensis subsp. bovis	strain=LMG 30663	GCA_018403725.1	1850438	1281486	type	True	78.5604	111	645	95	below_threshold
Lactococcus petauri	strain=159469	GCA_002154895.1	1940789	1940789	type	True	78.2597	120	645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:34,052] [INFO] DFAST Taxonomy check result was written to GCF_014905395.1_ASM1490539v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:34,052] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:34,053] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:34,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb68c4f6a-b156-47fc-981f-aa9d1674fe68/dqc_reference/checkm_data
[2024-01-25 19:36:34,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:34,075] [INFO] Task started: CheckM
[2024-01-25 19:36:34,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014905395.1_ASM1490539v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014905395.1_ASM1490539v1_genomic.fna/checkm_input GCF_014905395.1_ASM1490539v1_genomic.fna/checkm_result
[2024-01-25 19:36:51,468] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:51,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:51,488] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:51,488] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:51,488] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014905395.1_ASM1490539v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:51,489] [INFO] Task started: Blastn
[2024-01-25 19:36:51,489] [INFO] Running command: blastn -query GCF_014905395.1_ASM1490539v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb68c4f6a-b156-47fc-981f-aa9d1674fe68/dqc_reference/reference_markers_gtdb.fasta -out GCF_014905395.1_ASM1490539v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:52,276] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:52,279] [INFO] Selected 13 target genomes.
[2024-01-25 19:36:52,279] [INFO] Target genome list was writen to GCF_014905395.1_ASM1490539v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:52,286] [INFO] Task started: fastANI
[2024-01-25 19:36:52,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg1edac0e7-c015-4408-9cbe-909f738db45b/GCF_014905395.1_ASM1490539v1_genomic.fna.gz --refList GCF_014905395.1_ASM1490539v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014905395.1_ASM1490539v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:57,392] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:57,399] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:57,399] [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_014905395.1	s__Lactococcus taiwanensis	100.0	644	645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.39	0.94	0.93	6	conclusive
GCF_900099625.1	s__Lactococcus lactis	84.5649	326	645	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	81.9515	311	645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.76	97.45	0.91	0.82	70	-
GCF_004210295.1	s__Lactococcus sp004210295	81.6916	288	645	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	79.2822	219	645	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	79.0974	234	645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.72	98.72	0.90	0.90	2	-
GCF_009601055.1	s__Lactococcus sp009601055	78.5419	120	645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	100.00	99.99	0.99	0.98	3	-
GCF_016027715.1	s__Lactococcus garvieae_A	78.5084	119	645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.50	0.90	0.89	3	-
GCF_009601015.1	s__Lactococcus hircilactis	78.4247	118	645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154895.1	s__Lactococcus petauri	78.2286	121	645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.05	96.82	0.88	0.79	32	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:57,402] [INFO] GTDB search result was written to GCF_014905395.1_ASM1490539v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:57,402] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:57,405] [INFO] DFAST_QC result json was written to GCF_014905395.1_ASM1490539v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:57,405] [INFO] DFAST_QC completed!
[2024-01-25 19:36:57,405] [INFO] Total running time: 0h0m37s