[2023-06-05 02:12:13,268] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:12:13,272] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:12:13,273] [INFO] DQC Reference Directory: /var/lib/cwl/stgddc5d278-99a4-4759-bf5b-f348e320cc56/dqc_reference
[2023-06-05 02:12:15,600] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:12:15,601] [INFO] Task started: Prodigal
[2023-06-05 02:12:15,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg192bbd5e-4b20-468b-895c-f84b7c526b1d/GCA_934191635.1_ERR7747322_bin.145_genomic.fna.gz | prodigal -d GCA_934191635.1_ERR7747322_bin.145_genomic.fna/cds.fna -a GCA_934191635.1_ERR7747322_bin.145_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:12:20,249] [INFO] Task succeeded: Prodigal
[2023-06-05 02:12:20,250] [INFO] Task started: HMMsearch
[2023-06-05 02:12:20,250] [INFO] Running command: hmmsearch --tblout GCA_934191635.1_ERR7747322_bin.145_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddc5d278-99a4-4759-bf5b-f348e320cc56/dqc_reference/reference_markers.hmm GCA_934191635.1_ERR7747322_bin.145_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:12:20,507] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:12:20,509] [INFO] Found 6/6 markers.
[2023-06-05 02:12:20,535] [INFO] Query marker FASTA was written to GCA_934191635.1_ERR7747322_bin.145_genomic.fna/markers.fasta
[2023-06-05 02:12:20,536] [INFO] Task started: Blastn
[2023-06-05 02:12:20,536] [INFO] Running command: blastn -query GCA_934191635.1_ERR7747322_bin.145_genomic.fna/markers.fasta -db /var/lib/cwl/stgddc5d278-99a4-4759-bf5b-f348e320cc56/dqc_reference/reference_markers.fasta -out GCA_934191635.1_ERR7747322_bin.145_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:12:21,113] [INFO] Task succeeded: Blastn
[2023-06-05 02:12:21,118] [INFO] Selected 11 target genomes.
[2023-06-05 02:12:21,118] [INFO] Target genome list was writen to GCA_934191635.1_ERR7747322_bin.145_genomic.fna/target_genomes.txt
[2023-06-05 02:12:21,120] [INFO] Task started: fastANI
[2023-06-05 02:12:21,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg192bbd5e-4b20-468b-895c-f84b7c526b1d/GCA_934191635.1_ERR7747322_bin.145_genomic.fna.gz --refList GCA_934191635.1_ERR7747322_bin.145_genomic.fna/target_genomes.txt --output GCA_934191635.1_ERR7747322_bin.145_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:12:25,823] [INFO] Task succeeded: fastANI
[2023-06-05 02:12:25,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddc5d278-99a4-4759-bf5b-f348e320cc56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:12:25,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddc5d278-99a4-4759-bf5b-f348e320cc56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:12:25,832] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 02:12:25,832] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 02:12:25,832] [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 petauri	strain=159469	GCA_002154895.1	1940789	1940789	type	True	97.5548	600	696	95	conclusive
Lactococcus garvieae	strain=DSM 20684	GCA_002441675.1	1363	1363	type	True	93.0572	542	696	95	below_threshold
Lactococcus garvieae	strain=NBRC 100934	GCA_000739975.1	1363	1363	type	True	93.0526	550	696	95	below_threshold
Lactococcus garvieae subsp. garvieae	strain=CCUG 32208T	GCA_008692985.1	1890280	1363	type	True	93.0511	554	696	95	below_threshold
Lactococcus formosensis subsp. bovis	strain=LMG 30663	GCA_018403725.1	1850438	1281486	type	True	93.0506	546	696	95	below_threshold
Lactococcus formosensis	strain=NBRC 109475	GCA_018403745.1	1281486	1281486	type	True	92.8326	567	696	95	below_threshold
Lactococcus garvieae	strain=FDAARGOS_929	GCA_016026695.1	1363	1363	type	True	92.7978	576	696	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:12:25,835] [INFO] DFAST Taxonomy check result was written to GCA_934191635.1_ERR7747322_bin.145_genomic.fna/tc_result.tsv
[2023-06-05 02:12:25,835] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:12:25,835] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:12:25,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddc5d278-99a4-4759-bf5b-f348e320cc56/dqc_reference/checkm_data
[2023-06-05 02:12:25,836] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:12:25,863] [INFO] Task started: CheckM
[2023-06-05 02:12:25,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934191635.1_ERR7747322_bin.145_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934191635.1_ERR7747322_bin.145_genomic.fna/checkm_input GCA_934191635.1_ERR7747322_bin.145_genomic.fna/checkm_result
[2023-06-05 02:12:47,372] [INFO] Task succeeded: CheckM
[2023-06-05 02:12:47,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:12:47,394] [INFO] ===== Completeness check finished =====
[2023-06-05 02:12:47,395] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:12:47,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934191635.1_ERR7747322_bin.145_genomic.fna/markers.fasta)
[2023-06-05 02:12:47,395] [INFO] Task started: Blastn
[2023-06-05 02:12:47,396] [INFO] Running command: blastn -query GCA_934191635.1_ERR7747322_bin.145_genomic.fna/markers.fasta -db /var/lib/cwl/stgddc5d278-99a4-4759-bf5b-f348e320cc56/dqc_reference/reference_markers_gtdb.fasta -out GCA_934191635.1_ERR7747322_bin.145_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:12:48,133] [INFO] Task succeeded: Blastn
[2023-06-05 02:12:48,137] [INFO] Selected 9 target genomes.
[2023-06-05 02:12:48,137] [INFO] Target genome list was writen to GCA_934191635.1_ERR7747322_bin.145_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:12:48,193] [INFO] Task started: fastANI
[2023-06-05 02:12:48,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg192bbd5e-4b20-468b-895c-f84b7c526b1d/GCA_934191635.1_ERR7747322_bin.145_genomic.fna.gz --refList GCA_934191635.1_ERR7747322_bin.145_genomic.fna/target_genomes_gtdb.txt --output GCA_934191635.1_ERR7747322_bin.145_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:12:51,948] [INFO] Task succeeded: fastANI
[2023-06-05 02:12:51,960] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:12:51,960] [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_002154895.1	s__Lactococcus petauri	97.5548	600	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.05	96.82	0.88	0.79	32	conclusive
GCF_000739975.1	s__Lactococcus garvieae	93.0473	551	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.37	97.58	0.89	0.85	26	-
GCF_018403745.1	s__Lactococcus formosensis	92.8326	567	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.20	97.52	0.88	0.85	8	-
GCF_016758115.1	s__Lactococcus sp002492185	84.0644	389	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.71	98.67	0.89	0.88	5	-
GCF_016027715.1	s__Lactococcus garvieae_A	82.6347	449	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.50	0.90	0.89	3	-
GCF_001591705.1	s__Lactococcus cremoris	78.331	148	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.76	97.45	0.91	0.82	70	-
GCF_900104225.1	s__Streptococcus equinus_D	77.5488	50	696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:12:51,962] [INFO] GTDB search result was written to GCA_934191635.1_ERR7747322_bin.145_genomic.fna/result_gtdb.tsv
[2023-06-05 02:12:51,962] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:12:51,966] [INFO] DFAST_QC result json was written to GCA_934191635.1_ERR7747322_bin.145_genomic.fna/dqc_result.json
[2023-06-05 02:12:51,966] [INFO] DFAST_QC completed!
[2023-06-05 02:12:51,966] [INFO] Total running time: 0h0m39s