[2024-01-24 13:46:10,945] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:10,947] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:10,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg10a9c2b2-c229-494b-99a6-2e9e98fc09f1/dqc_reference
[2024-01-24 13:46:12,244] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:12,245] [INFO] Task started: Prodigal
[2024-01-24 13:46:12,245] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc4cb4b7-a781-41a3-b0c3-4b2dc9a93ad9/GCF_008692945.1_ASM869294v1_genomic.fna.gz | prodigal -d GCF_008692945.1_ASM869294v1_genomic.fna/cds.fna -a GCF_008692945.1_ASM869294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:17,310] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:17,311] [INFO] Task started: HMMsearch
[2024-01-24 13:46:17,311] [INFO] Running command: hmmsearch --tblout GCF_008692945.1_ASM869294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10a9c2b2-c229-494b-99a6-2e9e98fc09f1/dqc_reference/reference_markers.hmm GCF_008692945.1_ASM869294v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:17,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:17,604] [INFO] Found 6/6 markers.
[2024-01-24 13:46:17,634] [INFO] Query marker FASTA was written to GCF_008692945.1_ASM869294v1_genomic.fna/markers.fasta
[2024-01-24 13:46:17,635] [INFO] Task started: Blastn
[2024-01-24 13:46:17,635] [INFO] Running command: blastn -query GCF_008692945.1_ASM869294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10a9c2b2-c229-494b-99a6-2e9e98fc09f1/dqc_reference/reference_markers.fasta -out GCF_008692945.1_ASM869294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:18,233] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:18,236] [INFO] Selected 7 target genomes.
[2024-01-24 13:46:18,237] [INFO] Target genome list was writen to GCF_008692945.1_ASM869294v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:18,243] [INFO] Task started: fastANI
[2024-01-24 13:46:18,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc4cb4b7-a781-41a3-b0c3-4b2dc9a93ad9/GCF_008692945.1_ASM869294v1_genomic.fna.gz --refList GCF_008692945.1_ASM869294v1_genomic.fna/target_genomes.txt --output GCF_008692945.1_ASM869294v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:22,243] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:22,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10a9c2b2-c229-494b-99a6-2e9e98fc09f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:22,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10a9c2b2-c229-494b-99a6-2e9e98fc09f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:22,252] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:46:22,252] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:22,252] [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=CCUG 32210T	GCA_008692945.1	203404	1358	type	True	100.0	781	783	95	conclusive
Lactococcus lactis subsp. hordniae	strain=DSM 20450	GCA_002441785.1	203404	1358	type	True	99.9787	732	783	95	conclusive
Lactococcus lactis subsp. hordniae	strain=NBRC 100931	GCA_001591725.1	203404	1358	type	True	99.9758	750	783	95	conclusive
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_001456385.1	1360	1358	type	True	97.2617	632	783	95	conclusive
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_004354485.1	1360	1358	type	True	97.2037	646	783	95	conclusive
Lactococcus formosensis subsp. bovis	strain=LMG 30663	GCA_018403725.1	1850438	1281486	type	True	78.4971	128	783	95	below_threshold
Lactococcus paracarnosus	strain=TMW 2.1615	GCA_006770285.1	2749962	2749962	type	True	77.2378	54	783	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:22,254] [INFO] DFAST Taxonomy check result was written to GCF_008692945.1_ASM869294v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:22,255] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:22,255] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:22,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10a9c2b2-c229-494b-99a6-2e9e98fc09f1/dqc_reference/checkm_data
[2024-01-24 13:46:22,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:22,295] [INFO] Task started: CheckM
[2024-01-24 13:46:22,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008692945.1_ASM869294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008692945.1_ASM869294v1_genomic.fna/checkm_input GCF_008692945.1_ASM869294v1_genomic.fna/checkm_result
[2024-01-24 13:46:46,112] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:46,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:46,132] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:46,133] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:46,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008692945.1_ASM869294v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:46,134] [INFO] Task started: Blastn
[2024-01-24 13:46:46,134] [INFO] Running command: blastn -query GCF_008692945.1_ASM869294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10a9c2b2-c229-494b-99a6-2e9e98fc09f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_008692945.1_ASM869294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:46,979] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:46,984] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:46,984] [INFO] Target genome list was writen to GCF_008692945.1_ASM869294v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:47,001] [INFO] Task started: fastANI
[2024-01-24 13:46:47,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc4cb4b7-a781-41a3-b0c3-4b2dc9a93ad9/GCF_008692945.1_ASM869294v1_genomic.fna.gz --refList GCF_008692945.1_ASM869294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008692945.1_ASM869294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:54,111] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:54,128] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:54,129] [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	97.2278	639	783	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	87.4873	535	783	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	84.3718	336	783	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	81.375	337	783	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	79.0693	301	783	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	79.0044	308	783	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	78.7564	160	783	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	78.6112	128	783	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	78.2349	153	783	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	77.8825	173	783	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	77.5676	60	783	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	77.1587	62	783	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 13:46:54,130] [INFO] GTDB search result was written to GCF_008692945.1_ASM869294v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:54,131] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:54,134] [INFO] DFAST_QC result json was written to GCF_008692945.1_ASM869294v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:54,134] [INFO] DFAST_QC completed!
[2024-01-24 13:46:54,134] [INFO] Total running time: 0h0m43s