[2023-06-19 09:17:40,226] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:17:40,228] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:17:40,228] [INFO] DQC Reference Directory: /var/lib/cwl/stga3cccd06-d952-4496-9629-c4a97d37db47/dqc_reference
[2023-06-19 09:17:41,428] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:17:41,429] [INFO] Task started: Prodigal
[2023-06-19 09:17:41,429] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6b9995d-64b1-44ac-8904-c27626282257/GCA_018370895.1_ASM1837089v1_genomic.fna.gz | prodigal -d GCA_018370895.1_ASM1837089v1_genomic.fna/cds.fna -a GCA_018370895.1_ASM1837089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:17:46,760] [INFO] Task succeeded: Prodigal
[2023-06-19 09:17:46,760] [INFO] Task started: HMMsearch
[2023-06-19 09:17:46,760] [INFO] Running command: hmmsearch --tblout GCA_018370895.1_ASM1837089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3cccd06-d952-4496-9629-c4a97d37db47/dqc_reference/reference_markers.hmm GCA_018370895.1_ASM1837089v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:17:46,934] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:17:46,935] [INFO] Found 6/6 markers.
[2023-06-19 09:17:46,956] [INFO] Query marker FASTA was written to GCA_018370895.1_ASM1837089v1_genomic.fna/markers.fasta
[2023-06-19 09:17:46,957] [INFO] Task started: Blastn
[2023-06-19 09:17:46,957] [INFO] Running command: blastn -query GCA_018370895.1_ASM1837089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3cccd06-d952-4496-9629-c4a97d37db47/dqc_reference/reference_markers.fasta -out GCA_018370895.1_ASM1837089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:17:47,658] [INFO] Task succeeded: Blastn
[2023-06-19 09:17:47,665] [INFO] Selected 31 target genomes.
[2023-06-19 09:17:47,666] [INFO] Target genome list was writen to GCA_018370895.1_ASM1837089v1_genomic.fna/target_genomes.txt
[2023-06-19 09:17:47,671] [INFO] Task started: fastANI
[2023-06-19 09:17:47,671] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6b9995d-64b1-44ac-8904-c27626282257/GCA_018370895.1_ASM1837089v1_genomic.fna.gz --refList GCA_018370895.1_ASM1837089v1_genomic.fna/target_genomes.txt --output GCA_018370895.1_ASM1837089v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:18:02,974] [INFO] Task succeeded: fastANI
[2023-06-19 09:18:02,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3cccd06-d952-4496-9629-c4a97d37db47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:18:02,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3cccd06-d952-4496-9629-c4a97d37db47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:18:02,982] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:18:02,982] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 09:18:02,982] [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
Schaalia vaccimaxillae	strain=DSM 15804	GCA_000420425.1	183916	183916	type	True	78.3761	73	607	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	78.2193	87	607	95	below_threshold
Schaalia meyeri	strain=FDAARGOS_985	GCA_016127995.1	52773	52773	type	True	78.1623	90	607	95	below_threshold
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	77.7287	87	607	95	below_threshold
Schaalia suimastitidis	strain=DSM 15538	GCA_000429105.1	121163	121163	type	True	77.3629	58	607	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 09:18:02,984] [INFO] DFAST Taxonomy check result was written to GCA_018370895.1_ASM1837089v1_genomic.fna/tc_result.tsv
[2023-06-19 09:18:02,985] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:18:02,985] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:18:02,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3cccd06-d952-4496-9629-c4a97d37db47/dqc_reference/checkm_data
[2023-06-19 09:18:02,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:18:03,007] [INFO] Task started: CheckM
[2023-06-19 09:18:03,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018370895.1_ASM1837089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018370895.1_ASM1837089v1_genomic.fna/checkm_input GCA_018370895.1_ASM1837089v1_genomic.fna/checkm_result
[2023-06-19 09:18:24,502] [INFO] Task succeeded: CheckM
[2023-06-19 09:18:24,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:18:24,520] [INFO] ===== Completeness check finished =====
[2023-06-19 09:18:24,520] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:18:24,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018370895.1_ASM1837089v1_genomic.fna/markers.fasta)
[2023-06-19 09:18:24,521] [INFO] Task started: Blastn
[2023-06-19 09:18:24,521] [INFO] Running command: blastn -query GCA_018370895.1_ASM1837089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3cccd06-d952-4496-9629-c4a97d37db47/dqc_reference/reference_markers_gtdb.fasta -out GCA_018370895.1_ASM1837089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:18:25,455] [INFO] Task succeeded: Blastn
[2023-06-19 09:18:25,462] [INFO] Selected 11 target genomes.
[2023-06-19 09:18:25,462] [INFO] Target genome list was writen to GCA_018370895.1_ASM1837089v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:18:25,546] [INFO] Task started: fastANI
[2023-06-19 09:18:25,546] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6b9995d-64b1-44ac-8904-c27626282257/GCA_018370895.1_ASM1837089v1_genomic.fna.gz --refList GCA_018370895.1_ASM1837089v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018370895.1_ASM1837089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:18:32,152] [INFO] Task succeeded: fastANI
[2023-06-19 09:18:32,160] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:18:32,160] [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
GCA_900541895.1	s__Pauljensenia sp900541895	95.7564	543	607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.30	95.78	0.91	0.83	4	conclusive
GCF_000308055.1	s__Pauljensenia sp000308055	93.2356	565	607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.51	95.51	0.96	0.95	7	-
GCF_001070855.1	s__Pauljensenia pyogenes_A	93.1426	559	607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.06	97.06	0.98	0.98	2	-
GCA_900554605.1	s__Pauljensenia sp900554605	84.2134	218	607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758755.1	s__Pauljensenia sp000758755	84.1923	397	607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.30	97.11	0.96	0.96	3	-
GCF_900155605.1	s__Pauljensenia marseillensis	83.8692	408	607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002847525.1	s__Pauljensenia odontolytica_B	79.1894	117	607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.06	96.22	0.94	0.92	3	-
GCF_000466265.1	s__Pauljensenia sp000466265	79.0531	122	607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.80	96.80	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-19 09:18:32,163] [INFO] GTDB search result was written to GCA_018370895.1_ASM1837089v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:18:32,164] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:18:32,166] [INFO] DFAST_QC result json was written to GCA_018370895.1_ASM1837089v1_genomic.fna/dqc_result.json
[2023-06-19 09:18:32,166] [INFO] DFAST_QC completed!
[2023-06-19 09:18:32,166] [INFO] Total running time: 0h0m52s