[2024-01-25 20:14:50,442] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:50,444] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:50,444] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a563903-1bb2-4d54-9d4b-5b15d0e4bbeb/dqc_reference
[2024-01-25 20:14:51,594] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:51,595] [INFO] Task started: Prodigal
[2024-01-25 20:14:51,595] [INFO] Running command: gunzip -c /var/lib/cwl/stg83e0c2bc-0eb2-4398-845a-a94c549fe1ad/GCF_002441675.1_ASM244167v1_genomic.fna.gz | prodigal -d GCF_002441675.1_ASM244167v1_genomic.fna/cds.fna -a GCF_002441675.1_ASM244167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:55,571] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:55,572] [INFO] Task started: HMMsearch
[2024-01-25 20:14:55,572] [INFO] Running command: hmmsearch --tblout GCF_002441675.1_ASM244167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a563903-1bb2-4d54-9d4b-5b15d0e4bbeb/dqc_reference/reference_markers.hmm GCF_002441675.1_ASM244167v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:55,771] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:55,772] [INFO] Found 6/6 markers.
[2024-01-25 20:14:55,792] [INFO] Query marker FASTA was written to GCF_002441675.1_ASM244167v1_genomic.fna/markers.fasta
[2024-01-25 20:14:55,792] [INFO] Task started: Blastn
[2024-01-25 20:14:55,792] [INFO] Running command: blastn -query GCF_002441675.1_ASM244167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a563903-1bb2-4d54-9d4b-5b15d0e4bbeb/dqc_reference/reference_markers.fasta -out GCF_002441675.1_ASM244167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:56,334] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:56,337] [INFO] Selected 10 target genomes.
[2024-01-25 20:14:56,338] [INFO] Target genome list was writen to GCF_002441675.1_ASM244167v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:56,341] [INFO] Task started: fastANI
[2024-01-25 20:14:56,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e0c2bc-0eb2-4398-845a-a94c549fe1ad/GCF_002441675.1_ASM244167v1_genomic.fna.gz --refList GCF_002441675.1_ASM244167v1_genomic.fna/target_genomes.txt --output GCF_002441675.1_ASM244167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:00,908] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:00,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a563903-1bb2-4d54-9d4b-5b15d0e4bbeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:00,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a563903-1bb2-4d54-9d4b-5b15d0e4bbeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:00,915] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 20:15:00,915] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:00,915] [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 garvieae	strain=DSM 20684	GCA_002441675.1	1363	1363	type	True	100.0	641	642	95	conclusive
Lactococcus garvieae subsp. garvieae	strain=CCUG 32208T	GCA_008692985.1	1890280	1363	type	True	99.9989	637	642	95	conclusive
Lactococcus garvieae	strain=NBRC 100934	GCA_000739975.1	1363	1363	type	True	99.992	622	642	95	conclusive
Lactococcus garvieae	strain=FDAARGOS_929	GCA_016026695.1	1363	1363	type	True	99.9642	637	642	95	conclusive
Lactococcus petauri	strain=159469	GCA_002154895.1	1940789	1940789	type	True	92.8993	549	642	95	below_threshold
Lactococcus formosensis subsp. bovis	strain=LMG 30663	GCA_018403725.1	1850438	1281486	type	True	90.9441	534	642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:00,917] [INFO] DFAST Taxonomy check result was written to GCF_002441675.1_ASM244167v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:00,917] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:00,917] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:00,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a563903-1bb2-4d54-9d4b-5b15d0e4bbeb/dqc_reference/checkm_data
[2024-01-25 20:15:00,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:00,942] [INFO] Task started: CheckM
[2024-01-25 20:15:00,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002441675.1_ASM244167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002441675.1_ASM244167v1_genomic.fna/checkm_input GCF_002441675.1_ASM244167v1_genomic.fna/checkm_result
[2024-01-25 20:15:18,452] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:18,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:18,482] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:18,482] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:18,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002441675.1_ASM244167v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:18,482] [INFO] Task started: Blastn
[2024-01-25 20:15:18,482] [INFO] Running command: blastn -query GCF_002441675.1_ASM244167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a563903-1bb2-4d54-9d4b-5b15d0e4bbeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002441675.1_ASM244167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:19,283] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:19,285] [INFO] Selected 8 target genomes.
[2024-01-25 20:15:19,285] [INFO] Target genome list was writen to GCF_002441675.1_ASM244167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:19,298] [INFO] Task started: fastANI
[2024-01-25 20:15:19,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e0c2bc-0eb2-4398-845a-a94c549fe1ad/GCF_002441675.1_ASM244167v1_genomic.fna.gz --refList GCF_002441675.1_ASM244167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002441675.1_ASM244167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:22,896] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:22,900] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:22,900] [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_000739975.1	s__Lactococcus garvieae	99.992	622	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.37	97.58	0.89	0.85	26	conclusive
GCF_002154895.1	s__Lactococcus petauri	92.9052	548	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.05	96.82	0.88	0.79	32	-
GCF_018403745.1	s__Lactococcus formosensis	91.0537	544	642	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	83.7018	381	642	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	82.833	424	642	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.50	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:22,902] [INFO] GTDB search result was written to GCF_002441675.1_ASM244167v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:22,903] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:22,905] [INFO] DFAST_QC result json was written to GCF_002441675.1_ASM244167v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:22,905] [INFO] DFAST_QC completed!
[2024-01-25 20:15:22,905] [INFO] Total running time: 0h0m32s