[2024-01-24 11:05:24,330] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:24,332] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:24,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg424ffac6-9e12-4c39-90d3-0dd275bbb5d1/dqc_reference
[2024-01-24 11:05:25,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:25,559] [INFO] Task started: Prodigal
[2024-01-24 11:05:25,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg07c8ae2e-ad90-4783-89a4-344a56af1a57/GCF_023973165.1_ASM2397316v1_genomic.fna.gz | prodigal -d GCF_023973165.1_ASM2397316v1_genomic.fna/cds.fna -a GCF_023973165.1_ASM2397316v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:31,070] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:31,071] [INFO] Task started: HMMsearch
[2024-01-24 11:05:31,071] [INFO] Running command: hmmsearch --tblout GCF_023973165.1_ASM2397316v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg424ffac6-9e12-4c39-90d3-0dd275bbb5d1/dqc_reference/reference_markers.hmm GCF_023973165.1_ASM2397316v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:31,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:31,313] [INFO] Found 6/6 markers.
[2024-01-24 11:05:31,332] [INFO] Query marker FASTA was written to GCF_023973165.1_ASM2397316v1_genomic.fna/markers.fasta
[2024-01-24 11:05:31,332] [INFO] Task started: Blastn
[2024-01-24 11:05:31,332] [INFO] Running command: blastn -query GCF_023973165.1_ASM2397316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg424ffac6-9e12-4c39-90d3-0dd275bbb5d1/dqc_reference/reference_markers.fasta -out GCF_023973165.1_ASM2397316v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:31,945] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:31,949] [INFO] Selected 15 target genomes.
[2024-01-24 11:05:31,949] [INFO] Target genome list was writen to GCF_023973165.1_ASM2397316v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:31,967] [INFO] Task started: fastANI
[2024-01-24 11:05:31,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg07c8ae2e-ad90-4783-89a4-344a56af1a57/GCF_023973165.1_ASM2397316v1_genomic.fna.gz --refList GCF_023973165.1_ASM2397316v1_genomic.fna/target_genomes.txt --output GCF_023973165.1_ASM2397316v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:40,445] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:40,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg424ffac6-9e12-4c39-90d3-0dd275bbb5d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:40,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg424ffac6-9e12-4c39-90d3-0dd275bbb5d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:40,451] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:40,452] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:40,452] [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
Arcanobacterium pinnipediorum	strain=DSM 28752	GCA_023973165.1	1503041	1503041	type	True	100.0	648	650	95	conclusive
Arcanobacterium phocisimile	strain=DSM 26142	GCA_016904675.1	1302235	1302235	type	True	82.1572	327	650	95	below_threshold
Arcanobacterium phocae	strain=DSM 10002	GCA_900105865.1	131112	131112	suspected-type	True	81.8388	193	650	95	below_threshold
Arcanobacterium haemolyticum	strain=NCTC8452	GCA_900475915.1	28264	28264	type	True	79.6644	157	650	95	below_threshold
Arcanobacterium haemolyticum	strain=DSM 20595	GCA_000092365.1	28264	28264	type	True	79.5636	154	650	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:40,453] [INFO] DFAST Taxonomy check result was written to GCF_023973165.1_ASM2397316v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:40,454] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:40,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:40,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg424ffac6-9e12-4c39-90d3-0dd275bbb5d1/dqc_reference/checkm_data
[2024-01-24 11:05:40,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:40,502] [INFO] Task started: CheckM
[2024-01-24 11:05:40,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023973165.1_ASM2397316v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023973165.1_ASM2397316v1_genomic.fna/checkm_input GCF_023973165.1_ASM2397316v1_genomic.fna/checkm_result
[2024-01-24 11:06:04,013] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:04,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:04,053] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:04,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:04,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023973165.1_ASM2397316v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:04,054] [INFO] Task started: Blastn
[2024-01-24 11:06:04,054] [INFO] Running command: blastn -query GCF_023973165.1_ASM2397316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg424ffac6-9e12-4c39-90d3-0dd275bbb5d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_023973165.1_ASM2397316v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:04,969] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:04,973] [INFO] Selected 18 target genomes.
[2024-01-24 11:06:04,974] [INFO] Target genome list was writen to GCF_023973165.1_ASM2397316v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:05,019] [INFO] Task started: fastANI
[2024-01-24 11:06:05,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg07c8ae2e-ad90-4783-89a4-344a56af1a57/GCF_023973165.1_ASM2397316v1_genomic.fna.gz --refList GCF_023973165.1_ASM2397316v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023973165.1_ASM2397316v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:13,396] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:13,402] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:06:13,402] [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_016904675.1	s__Arcanobacterium phocisimile	82.2124	326	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105865.1	s__Arcanobacterium phocae	82.0019	195	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	99.03	98.90	0.93	0.90	5	-
GCF_012563545.1	s__Arcanobacterium sp012563545	81.7339	204	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018913465.1	s__Arcanobacterium phocae_A	79.4613	176	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	96.34	96.10	0.91	0.89	37	-
GCF_000092365.1	s__Arcanobacterium haemolyticum	79.4129	152	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	99.39	98.67	0.98	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:13,404] [INFO] GTDB search result was written to GCF_023973165.1_ASM2397316v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:13,404] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:13,407] [INFO] DFAST_QC result json was written to GCF_023973165.1_ASM2397316v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:13,407] [INFO] DFAST_QC completed!
[2024-01-24 11:06:13,407] [INFO] Total running time: 0h0m49s