[2024-01-24 15:03:29,339] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:29,340] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:29,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg591ae626-977a-41d4-a7f6-f2af273c97f2/dqc_reference
[2024-01-24 15:03:32,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:32,683] [INFO] Task started: Prodigal
[2024-01-24 15:03:32,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg23ea4091-e88f-41bd-a5d8-5bff8ebdec59/GCF_014202895.1_ASM1420289v1_genomic.fna.gz | prodigal -d GCF_014202895.1_ASM1420289v1_genomic.fna/cds.fna -a GCF_014202895.1_ASM1420289v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:35,662] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:35,663] [INFO] Task started: HMMsearch
[2024-01-24 15:03:35,663] [INFO] Running command: hmmsearch --tblout GCF_014202895.1_ASM1420289v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg591ae626-977a-41d4-a7f6-f2af273c97f2/dqc_reference/reference_markers.hmm GCF_014202895.1_ASM1420289v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:35,895] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:35,896] [INFO] Found 6/6 markers.
[2024-01-24 15:03:35,912] [INFO] Query marker FASTA was written to GCF_014202895.1_ASM1420289v1_genomic.fna/markers.fasta
[2024-01-24 15:03:35,913] [INFO] Task started: Blastn
[2024-01-24 15:03:35,913] [INFO] Running command: blastn -query GCF_014202895.1_ASM1420289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg591ae626-977a-41d4-a7f6-f2af273c97f2/dqc_reference/reference_markers.fasta -out GCF_014202895.1_ASM1420289v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:38,854] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:38,856] [INFO] Selected 28 target genomes.
[2024-01-24 15:03:38,857] [INFO] Target genome list was writen to GCF_014202895.1_ASM1420289v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:38,864] [INFO] Task started: fastANI
[2024-01-24 15:03:38,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg23ea4091-e88f-41bd-a5d8-5bff8ebdec59/GCF_014202895.1_ASM1420289v1_genomic.fna.gz --refList GCF_014202895.1_ASM1420289v1_genomic.fna/target_genomes.txt --output GCF_014202895.1_ASM1420289v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:48,151] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:48,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg591ae626-977a-41d4-a7f6-f2af273c97f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:48,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg591ae626-977a-41d4-a7f6-f2af273c97f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:48,187] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:48,187] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:48,187] [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
Lactovum miscens	strain=DSM 14925	GCA_014202895.1	190387	190387	type	True	100.0	550	551	95	conclusive
Lactococcus lactis	strain=ATCC 19435	GCA_900099625.1	1358	1358	type	True	77.3283	54	551	95	below_threshold
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_001456385.1	1360	1358	type	True	77.2277	51	551	95	below_threshold
Lactococcus lactis subsp. lactis	strain=NBRC 100933	GCA_001514475.1	1360	1358	suspected-type	True	77.2091	52	551	95	below_threshold
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_004354485.1	1360	1358	type	True	77.1764	52	551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:48,188] [INFO] DFAST Taxonomy check result was written to GCF_014202895.1_ASM1420289v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:48,189] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:48,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:48,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg591ae626-977a-41d4-a7f6-f2af273c97f2/dqc_reference/checkm_data
[2024-01-24 15:03:48,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:48,214] [INFO] Task started: CheckM
[2024-01-24 15:03:48,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202895.1_ASM1420289v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202895.1_ASM1420289v1_genomic.fna/checkm_input GCF_014202895.1_ASM1420289v1_genomic.fna/checkm_result
[2024-01-24 15:04:08,361] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:08,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:08,375] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:08,376] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:08,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202895.1_ASM1420289v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:08,377] [INFO] Task started: Blastn
[2024-01-24 15:04:08,377] [INFO] Running command: blastn -query GCF_014202895.1_ASM1420289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg591ae626-977a-41d4-a7f6-f2af273c97f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202895.1_ASM1420289v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:09,389] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:09,392] [INFO] Selected 27 target genomes.
[2024-01-24 15:04:09,392] [INFO] Target genome list was writen to GCF_014202895.1_ASM1420289v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:09,407] [INFO] Task started: fastANI
[2024-01-24 15:04:09,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg23ea4091-e88f-41bd-a5d8-5bff8ebdec59/GCF_014202895.1_ASM1420289v1_genomic.fna.gz --refList GCF_014202895.1_ASM1420289v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202895.1_ASM1420289v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:19,235] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:19,244] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:19,244] [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_014202895.1	s__Lactovum miscens	100.0	550	551	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactovum	95.0	98.66	98.66	0.89	0.89	2	conclusive
GCF_900099625.1	s__Lactococcus lactis	77.3283	54	551	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.37	97.03	0.87	0.82	223	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:19,245] [INFO] GTDB search result was written to GCF_014202895.1_ASM1420289v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:19,246] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:19,248] [INFO] DFAST_QC result json was written to GCF_014202895.1_ASM1420289v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:19,248] [INFO] DFAST_QC completed!
[2024-01-24 15:04:19,248] [INFO] Total running time: 0h0m50s