[2024-01-24 12:31:34,779] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,781] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,782] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5d248f8-659c-49ee-8243-31dd564dd95e/dqc_reference
[2024-01-24 12:31:36,135] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:36,136] [INFO] Task started: Prodigal
[2024-01-24 12:31:36,137] [INFO] Running command: gunzip -c /var/lib/cwl/stg303947db-c559-49e0-9339-941dc27af1de/GCF_001552295.1_ASM155229v1_genomic.fna.gz | prodigal -d GCF_001552295.1_ASM155229v1_genomic.fna/cds.fna -a GCF_001552295.1_ASM155229v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:40,091] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:40,092] [INFO] Task started: HMMsearch
[2024-01-24 12:31:40,092] [INFO] Running command: hmmsearch --tblout GCF_001552295.1_ASM155229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5d248f8-659c-49ee-8243-31dd564dd95e/dqc_reference/reference_markers.hmm GCF_001552295.1_ASM155229v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:40,378] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:40,379] [INFO] Found 6/6 markers.
[2024-01-24 12:31:40,405] [INFO] Query marker FASTA was written to GCF_001552295.1_ASM155229v1_genomic.fna/markers.fasta
[2024-01-24 12:31:40,405] [INFO] Task started: Blastn
[2024-01-24 12:31:40,406] [INFO] Running command: blastn -query GCF_001552295.1_ASM155229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5d248f8-659c-49ee-8243-31dd564dd95e/dqc_reference/reference_markers.fasta -out GCF_001552295.1_ASM155229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:41,062] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:41,065] [INFO] Selected 24 target genomes.
[2024-01-24 12:31:41,065] [INFO] Target genome list was writen to GCF_001552295.1_ASM155229v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:41,093] [INFO] Task started: fastANI
[2024-01-24 12:31:41,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg303947db-c559-49e0-9339-941dc27af1de/GCF_001552295.1_ASM155229v1_genomic.fna.gz --refList GCF_001552295.1_ASM155229v1_genomic.fna/target_genomes.txt --output GCF_001552295.1_ASM155229v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:50,321] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:50,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5d248f8-659c-49ee-8243-31dd564dd95e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:50,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5d248f8-659c-49ee-8243-31dd564dd95e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:50,328] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:50,329] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:50,329] [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
Globicatella sanguinis	strain=NBRC 15551	GCA_001552295.1	13076	13076	type	True	100.0	656	661	95	conclusive
Globicatella sulfidifaciens	strain=DSM 15739	GCA_900167405.1	136093	136093	type	True	94.8109	528	661	95	below_threshold
Ruoffia halotolerans	strain=INB8	GCA_014049385.1	2748684	2748684	type	True	79.4827	65	661	95	below_threshold
Eremococcus coleocola	strain=DSM 15696	GCA_000428865.1	88132	88132	type	True	78.5726	63	661	95	below_threshold
Fundicoccus ignavus	strain=DSM 109652	GCA_009659375.1	2664442	2664442	type	True	78.2832	74	661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:50,330] [INFO] DFAST Taxonomy check result was written to GCF_001552295.1_ASM155229v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:50,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:50,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:50,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5d248f8-659c-49ee-8243-31dd564dd95e/dqc_reference/checkm_data
[2024-01-24 12:31:50,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:50,363] [INFO] Task started: CheckM
[2024-01-24 12:31:50,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552295.1_ASM155229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552295.1_ASM155229v1_genomic.fna/checkm_input GCF_001552295.1_ASM155229v1_genomic.fna/checkm_result
[2024-01-24 12:32:09,670] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:09,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:09,695] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:09,696] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:09,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552295.1_ASM155229v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:09,697] [INFO] Task started: Blastn
[2024-01-24 12:32:09,697] [INFO] Running command: blastn -query GCF_001552295.1_ASM155229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5d248f8-659c-49ee-8243-31dd564dd95e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552295.1_ASM155229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:10,482] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:10,486] [INFO] Selected 14 target genomes.
[2024-01-24 12:32:10,487] [INFO] Target genome list was writen to GCF_001552295.1_ASM155229v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:10,498] [INFO] Task started: fastANI
[2024-01-24 12:32:10,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg303947db-c559-49e0-9339-941dc27af1de/GCF_001552295.1_ASM155229v1_genomic.fna.gz --refList GCF_001552295.1_ASM155229v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552295.1_ASM155229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:16,739] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:16,750] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:16,750] [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_001552295.1	s__Globicatella sanguinis	100.0	656	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella	95.0	97.13	96.22	0.85	0.84	3	conclusive
GCF_900167405.1	s__Globicatella sulfidifaciens	94.8109	528	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella	95.0	97.81	97.81	0.71	0.71	2	-
GCA_014049385.1	s__Facklamia_A sp014049385	79.4827	65	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Facklamia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005864045.1	s__Facklamia_A tabacinasalis	78.5465	55	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Facklamia_A	95.0	96.44	96.27	0.84	0.80	4	-
GCA_016237705.1	s__Globicatella sp010892315	78.5264	141	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella	95.0	98.61	97.07	0.93	0.84	6	-
GCA_016126655.1	s__Globicatella sp016126655	78.4904	127	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella	95.0	98.94	98.51	0.93	0.88	6	-
GCF_009659375.1	s__Fundicoccus ignavus	78.2832	74	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Fundicoccus	95.0	98.16	98.10	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:16,752] [INFO] GTDB search result was written to GCF_001552295.1_ASM155229v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:16,752] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:16,755] [INFO] DFAST_QC result json was written to GCF_001552295.1_ASM155229v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:16,755] [INFO] DFAST_QC completed!
[2024-01-24 12:32:16,755] [INFO] Total running time: 0h0m42s