[2024-01-24 14:20:14,290] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,292] [INFO] DQC Reference Directory: /var/lib/cwl/stg4615ce57-ce60-495a-b9d4-09022258de6c/dqc_reference
[2024-01-24 14:20:15,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:15,623] [INFO] Task started: Prodigal
[2024-01-24 14:20:15,623] [INFO] Running command: gunzip -c /var/lib/cwl/stg86d7318b-5cc6-49d4-8747-edca62db4632/GCF_000429105.1_ASM42910v1_genomic.fna.gz | prodigal -d GCF_000429105.1_ASM42910v1_genomic.fna/cds.fna -a GCF_000429105.1_ASM42910v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:23,992] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:23,993] [INFO] Task started: HMMsearch
[2024-01-24 14:20:23,993] [INFO] Running command: hmmsearch --tblout GCF_000429105.1_ASM42910v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4615ce57-ce60-495a-b9d4-09022258de6c/dqc_reference/reference_markers.hmm GCF_000429105.1_ASM42910v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:24,200] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:24,201] [INFO] Found 6/6 markers.
[2024-01-24 14:20:24,230] [INFO] Query marker FASTA was written to GCF_000429105.1_ASM42910v1_genomic.fna/markers.fasta
[2024-01-24 14:20:24,230] [INFO] Task started: Blastn
[2024-01-24 14:20:24,230] [INFO] Running command: blastn -query GCF_000429105.1_ASM42910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4615ce57-ce60-495a-b9d4-09022258de6c/dqc_reference/reference_markers.fasta -out GCF_000429105.1_ASM42910v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:25,019] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:25,023] [INFO] Selected 16 target genomes.
[2024-01-24 14:20:25,023] [INFO] Target genome list was writen to GCF_000429105.1_ASM42910v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:25,043] [INFO] Task started: fastANI
[2024-01-24 14:20:25,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d7318b-5cc6-49d4-8747-edca62db4632/GCF_000429105.1_ASM42910v1_genomic.fna.gz --refList GCF_000429105.1_ASM42910v1_genomic.fna/target_genomes.txt --output GCF_000429105.1_ASM42910v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:34,075] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:34,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4615ce57-ce60-495a-b9d4-09022258de6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:34,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4615ce57-ce60-495a-b9d4-09022258de6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:34,082] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:34,082] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:34,082] [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 suimastitidis	strain=DSM 15538	GCA_000429105.1	121163	121163	type	True	100.0	759	759	95	conclusive
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	78.1067	71	759	95	below_threshold
Schaalia vaccimaxillae	strain=DSM 15804	GCA_000420425.1	183916	183916	type	True	77.4191	87	759	95	below_threshold
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	76.9408	62	759	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	76.8161	71	759	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:34,084] [INFO] DFAST Taxonomy check result was written to GCF_000429105.1_ASM42910v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:34,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:34,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:34,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4615ce57-ce60-495a-b9d4-09022258de6c/dqc_reference/checkm_data
[2024-01-24 14:20:34,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:34,110] [INFO] Task started: CheckM
[2024-01-24 14:20:34,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429105.1_ASM42910v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429105.1_ASM42910v1_genomic.fna/checkm_input GCF_000429105.1_ASM42910v1_genomic.fna/checkm_result
[2024-01-24 14:21:02,673] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:02,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:02,690] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:02,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:02,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429105.1_ASM42910v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:02,691] [INFO] Task started: Blastn
[2024-01-24 14:21:02,691] [INFO] Running command: blastn -query GCF_000429105.1_ASM42910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4615ce57-ce60-495a-b9d4-09022258de6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429105.1_ASM42910v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:03,656] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:03,659] [INFO] Selected 22 target genomes.
[2024-01-24 14:21:03,660] [INFO] Target genome list was writen to GCF_000429105.1_ASM42910v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:03,731] [INFO] Task started: fastANI
[2024-01-24 14:21:03,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d7318b-5cc6-49d4-8747-edca62db4632/GCF_000429105.1_ASM42910v1_genomic.fna.gz --refList GCF_000429105.1_ASM42910v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429105.1_ASM42910v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:12,598] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:12,611] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:12,611] [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_000429105.1	s__Pauljensenia suimastitidis	100.0	759	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000308055.1	s__Pauljensenia sp000308055	78.6404	57	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.51	95.51	0.96	0.95	7	-
GCF_013407865.1	s__Pauljensenia turicensis	78.2218	67	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.58	95.65	0.91	0.83	6	-
GCF_900155605.1	s__Pauljensenia marseillensis	78.1074	67	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	99.98	99.98	1.00	1.00	2	-
GCA_001072465.1	s__Pauljensenia sp001072465	78.0031	63	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCF_003858455.1	s__Pauljensenia canis	77.9626	89	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005696695.1	s__Pauljensenia odontolytica_C	77.9362	69	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.76	95.52	0.95	0.90	3	-
GCF_011038885.2	s__Pauljensenia sp011038875	77.7622	74	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	98.18	98.18	0.90	0.90	2	-
GCF_903645355.1	s__Pauljensenia sp903645355	77.7043	103	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405145.1	s__Pauljensenia cardiffensis	77.603	69	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.37	97.30	0.94	0.93	4	-
GCF_000420425.1	s__Pauljensenia vaccimaxillae	77.4191	87	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466265.1	s__Pauljensenia sp000466265	77.3658	72	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.80	96.80	0.90	0.90	2	-
GCA_018375675.1	s__Pauljensenia sp018375675	77.2427	70	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902373435.1	s__Pauljensenia sp902373435	77.1818	59	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.35	95.27	0.85	0.81	3	-
GCF_000758755.1	s__Pauljensenia sp000758755	76.9944	70	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.30	97.11	0.96	0.96	3	-
GCF_000429245.1	s__Pauljensenia georgiae	76.8636	69	759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.90	96.98	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:12,612] [INFO] GTDB search result was written to GCF_000429105.1_ASM42910v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:12,613] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:12,616] [INFO] DFAST_QC result json was written to GCF_000429105.1_ASM42910v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:12,616] [INFO] DFAST_QC completed!
[2024-01-24 14:21:12,616] [INFO] Total running time: 0h0m58s