[2024-01-25 20:25:35,614] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:25:35,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:25:35,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bc673f3-f08e-4c2d-bb0f-5a21ed305e50/dqc_reference
[2024-01-25 20:25:36,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:25:36,811] [INFO] Task started: Prodigal
[2024-01-25 20:25:36,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg25e6175b-0cd6-4944-bd23-35fe2ef0658b/GCF_900604515.1_PRJEB25658_genomic.fna.gz | prodigal -d GCF_900604515.1_PRJEB25658_genomic.fna/cds.fna -a GCF_900604515.1_PRJEB25658_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:25:41,535] [INFO] Task succeeded: Prodigal
[2024-01-25 20:25:41,535] [INFO] Task started: HMMsearch
[2024-01-25 20:25:41,535] [INFO] Running command: hmmsearch --tblout GCF_900604515.1_PRJEB25658_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bc673f3-f08e-4c2d-bb0f-5a21ed305e50/dqc_reference/reference_markers.hmm GCF_900604515.1_PRJEB25658_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:25:41,708] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:25:41,709] [INFO] Found 6/6 markers.
[2024-01-25 20:25:41,728] [INFO] Query marker FASTA was written to GCF_900604515.1_PRJEB25658_genomic.fna/markers.fasta
[2024-01-25 20:25:41,728] [INFO] Task started: Blastn
[2024-01-25 20:25:41,729] [INFO] Running command: blastn -query GCF_900604515.1_PRJEB25658_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bc673f3-f08e-4c2d-bb0f-5a21ed305e50/dqc_reference/reference_markers.fasta -out GCF_900604515.1_PRJEB25658_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:25:42,283] [INFO] Task succeeded: Blastn
[2024-01-25 20:25:42,286] [INFO] Selected 19 target genomes.
[2024-01-25 20:25:42,286] [INFO] Target genome list was writen to GCF_900604515.1_PRJEB25658_genomic.fna/target_genomes.txt
[2024-01-25 20:25:42,330] [INFO] Task started: fastANI
[2024-01-25 20:25:42,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e6175b-0cd6-4944-bd23-35fe2ef0658b/GCF_900604515.1_PRJEB25658_genomic.fna.gz --refList GCF_900604515.1_PRJEB25658_genomic.fna/target_genomes.txt --output GCF_900604515.1_PRJEB25658_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:25:53,665] [INFO] Task succeeded: fastANI
[2024-01-25 20:25:53,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bc673f3-f08e-4c2d-bb0f-5a21ed305e50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:25:53,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bc673f3-f08e-4c2d-bb0f-5a21ed305e50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:25:53,671] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:25:53,671] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:25:53,671] [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 ihumii	strain=Marseille-P5647	GCA_900604515.1	2138162	2138162	type	True	100.0	665	665	95	conclusive
Arcanobacterium bovis	strain=C605018/01/1	GCA_004331995.1	2529275	2529275	type	True	80.5872	208	665	95	below_threshold
Arcanobacterium pluranimalium	strain=DSM 13483	GCA_016907845.1	108028	108028	type	True	80.0635	209	665	95	below_threshold
Arcanobacterium haemolyticum	strain=DSM 20595	GCA_000092365.1	28264	28264	type	True	78.3013	61	665	95	below_threshold
Arcanobacterium haemolyticum	strain=NCTC8452	GCA_900475915.1	28264	28264	type	True	78.2047	63	665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:25:53,673] [INFO] DFAST Taxonomy check result was written to GCF_900604515.1_PRJEB25658_genomic.fna/tc_result.tsv
[2024-01-25 20:25:53,673] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:25:53,673] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:25:53,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bc673f3-f08e-4c2d-bb0f-5a21ed305e50/dqc_reference/checkm_data
[2024-01-25 20:25:53,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:25:53,698] [INFO] Task started: CheckM
[2024-01-25 20:25:53,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900604515.1_PRJEB25658_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900604515.1_PRJEB25658_genomic.fna/checkm_input GCF_900604515.1_PRJEB25658_genomic.fna/checkm_result
[2024-01-25 20:26:13,040] [INFO] Task succeeded: CheckM
[2024-01-25 20:26:13,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:26:13,055] [INFO] ===== Completeness check finished =====
[2024-01-25 20:26:13,055] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:26:13,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900604515.1_PRJEB25658_genomic.fna/markers.fasta)
[2024-01-25 20:26:13,056] [INFO] Task started: Blastn
[2024-01-25 20:26:13,056] [INFO] Running command: blastn -query GCF_900604515.1_PRJEB25658_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bc673f3-f08e-4c2d-bb0f-5a21ed305e50/dqc_reference/reference_markers_gtdb.fasta -out GCF_900604515.1_PRJEB25658_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:13,805] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:13,808] [INFO] Selected 24 target genomes.
[2024-01-25 20:26:13,808] [INFO] Target genome list was writen to GCF_900604515.1_PRJEB25658_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:26:13,875] [INFO] Task started: fastANI
[2024-01-25 20:26:13,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e6175b-0cd6-4944-bd23-35fe2ef0658b/GCF_900604515.1_PRJEB25658_genomic.fna.gz --refList GCF_900604515.1_PRJEB25658_genomic.fna/target_genomes_gtdb.txt --output GCF_900604515.1_PRJEB25658_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:26:25,132] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:25,137] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:26:25,137] [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_900604515.1	s__Arcanobacterium_A ihumii	100.0	665	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004331995.1	s__Arcanobacterium_A bovis	80.5872	208	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907845.1	s__Arcanobacterium_A pluranimalium	80.0893	208	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092365.1	s__Arcanobacterium haemolyticum	78.3013	61	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	99.39	98.67	0.98	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:26:25,138] [INFO] GTDB search result was written to GCF_900604515.1_PRJEB25658_genomic.fna/result_gtdb.tsv
[2024-01-25 20:26:25,139] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:26:25,141] [INFO] DFAST_QC result json was written to GCF_900604515.1_PRJEB25658_genomic.fna/dqc_result.json
[2024-01-25 20:26:25,141] [INFO] DFAST_QC completed!
[2024-01-25 20:26:25,141] [INFO] Total running time: 0h0m50s