[2023-06-13 19:58:24,519] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:58:24,522] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:58:24,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg210ccab0-dcbf-4734-bb35-a597ba4d4285/dqc_reference
[2023-06-13 19:58:25,802] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:58:25,802] [INFO] Task started: Prodigal
[2023-06-13 19:58:25,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg522f7ea0-90ef-46b4-b9b8-9d1b171e25f3/GCA_022654475.1_ASM2265447v1_genomic.fna.gz | prodigal -d GCA_022654475.1_ASM2265447v1_genomic.fna/cds.fna -a GCA_022654475.1_ASM2265447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:58:29,696] [INFO] Task succeeded: Prodigal
[2023-06-13 19:58:29,696] [INFO] Task started: HMMsearch
[2023-06-13 19:58:29,696] [INFO] Running command: hmmsearch --tblout GCA_022654475.1_ASM2265447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg210ccab0-dcbf-4734-bb35-a597ba4d4285/dqc_reference/reference_markers.hmm GCA_022654475.1_ASM2265447v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:58:29,909] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:58:29,911] [INFO] Found 6/6 markers.
[2023-06-13 19:58:29,933] [INFO] Query marker FASTA was written to GCA_022654475.1_ASM2265447v1_genomic.fna/markers.fasta
[2023-06-13 19:58:29,933] [INFO] Task started: Blastn
[2023-06-13 19:58:29,934] [INFO] Running command: blastn -query GCA_022654475.1_ASM2265447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg210ccab0-dcbf-4734-bb35-a597ba4d4285/dqc_reference/reference_markers.fasta -out GCA_022654475.1_ASM2265447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:58:30,535] [INFO] Task succeeded: Blastn
[2023-06-13 19:58:30,539] [INFO] Selected 15 target genomes.
[2023-06-13 19:58:30,539] [INFO] Target genome list was writen to GCA_022654475.1_ASM2265447v1_genomic.fna/target_genomes.txt
[2023-06-13 19:58:30,541] [INFO] Task started: fastANI
[2023-06-13 19:58:30,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg522f7ea0-90ef-46b4-b9b8-9d1b171e25f3/GCA_022654475.1_ASM2265447v1_genomic.fna.gz --refList GCA_022654475.1_ASM2265447v1_genomic.fna/target_genomes.txt --output GCA_022654475.1_ASM2265447v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:58:36,666] [INFO] Task succeeded: fastANI
[2023-06-13 19:58:36,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg210ccab0-dcbf-4734-bb35-a597ba4d4285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:58:36,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg210ccab0-dcbf-4734-bb35-a597ba4d4285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:58:36,677] [INFO] Found 10 fastANI hits (8 hits with ANI > threshold)
[2023-06-13 19:58:36,677] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 19:58:36,677] [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. lactis	strain=NBRC 100933	GCA_001514475.1	1360	1358	suspected-type	True	97.7114	563	657	95	conclusive
Lactococcus lactis	strain=ATCC 19435	GCA_900099625.1	1358	1358	type	True	97.6765	561	657	95	conclusive
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_004354485.1	1360	1358	type	True	97.6761	562	657	95	conclusive
Lactococcus lactis	strain=FDAARGOS_865	GCA_016028835.1	1358	1358	type	True	97.6735	570	657	95	conclusive
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_001456385.1	1360	1358	type	True	97.6324	557	657	95	conclusive
Lactococcus lactis subsp. hordniae	strain=CCUG 32210T	GCA_008692945.1	203404	1358	type	True	97.3488	532	657	95	conclusive
Lactococcus lactis subsp. hordniae	strain=DSM 20450	GCA_002441785.1	203404	1358	type	True	97.3251	537	657	95	conclusive
Lactococcus lactis subsp. hordniae	strain=NBRC 100931	GCA_001591725.1	203404	1358	type	True	97.2364	533	657	95	conclusive
Lactococcus formosensis subsp. bovis	strain=LMG 30663	GCA_018403725.1	1850438	1281486	type	True	78.9956	108	657	95	below_threshold
Lactococcus piscium	strain=DSM 6634	GCA_002441695.1	1364	1364	suspected-type	True	76.7813	54	657	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 19:58:36,679] [INFO] DFAST Taxonomy check result was written to GCA_022654475.1_ASM2265447v1_genomic.fna/tc_result.tsv
[2023-06-13 19:58:36,680] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:58:36,680] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:58:36,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg210ccab0-dcbf-4734-bb35-a597ba4d4285/dqc_reference/checkm_data
[2023-06-13 19:58:36,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:58:36,705] [INFO] Task started: CheckM
[2023-06-13 19:58:36,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022654475.1_ASM2265447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022654475.1_ASM2265447v1_genomic.fna/checkm_input GCA_022654475.1_ASM2265447v1_genomic.fna/checkm_result
[2023-06-13 19:58:56,071] [INFO] Task succeeded: CheckM
[2023-06-13 19:58:56,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 19:58:56,092] [INFO] ===== Completeness check finished =====
[2023-06-13 19:58:56,093] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:58:56,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022654475.1_ASM2265447v1_genomic.fna/markers.fasta)
[2023-06-13 19:58:56,093] [INFO] Task started: Blastn
[2023-06-13 19:58:56,093] [INFO] Running command: blastn -query GCA_022654475.1_ASM2265447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg210ccab0-dcbf-4734-bb35-a597ba4d4285/dqc_reference/reference_markers_gtdb.fasta -out GCA_022654475.1_ASM2265447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:58:57,030] [INFO] Task succeeded: Blastn
[2023-06-13 19:58:57,034] [INFO] Selected 20 target genomes.
[2023-06-13 19:58:57,035] [INFO] Target genome list was writen to GCA_022654475.1_ASM2265447v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:58:57,040] [INFO] Task started: fastANI
[2023-06-13 19:58:57,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg522f7ea0-90ef-46b4-b9b8-9d1b171e25f3/GCA_022654475.1_ASM2265447v1_genomic.fna.gz --refList GCA_022654475.1_ASM2265447v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022654475.1_ASM2265447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:59:05,361] [INFO] Task succeeded: fastANI
[2023-06-13 19:59:05,373] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 19:59:05,373] [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	97.6685	561	657	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	87.3296	489	657	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	84.5054	297	657	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	81.2784	306	657	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	79.495	265	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.72	98.72	0.90	0.90	2	-
GCF_003627095.1	s__Lactococcus allomyrinae	79.3563	272	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016027715.1	s__Lactococcus garvieae_A	78.8982	125	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.50	0.90	0.89	3	-
GCF_018403745.1	s__Lactococcus formosensis	78.8307	116	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.20	97.52	0.88	0.85	8	-
GCF_009601015.1	s__Lactococcus hircilactis	78.6628	152	657	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	78.2132	154	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	100.00	99.99	0.99	0.98	3	-
GCF_900104225.1	s__Streptococcus equinus_D	77.5115	56	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000283635.1	s__Streptococcus macedonicus	77.0581	56	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
GCF_002441695.1	s__Lactococcus_A piscium	76.7813	54	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 19:59:05,375] [INFO] GTDB search result was written to GCA_022654475.1_ASM2265447v1_genomic.fna/result_gtdb.tsv
[2023-06-13 19:59:05,376] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:59:05,379] [INFO] DFAST_QC result json was written to GCA_022654475.1_ASM2265447v1_genomic.fna/dqc_result.json
[2023-06-13 19:59:05,379] [INFO] DFAST_QC completed!
[2023-06-13 19:59:05,379] [INFO] Total running time: 0h0m41s