[2024-01-25 18:42:21,705] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:21,707] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:21,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg453dfc2c-5ad2-410c-aace-88a4dfe77b77/dqc_reference
[2024-01-25 18:42:22,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:22,837] [INFO] Task started: Prodigal
[2024-01-25 18:42:22,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg323db889-1353-45a6-bced-19ee7347b10d/GCF_900155635.1_Olsenella_urinainfantis_genomic.fna.gz | prodigal -d GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/cds.fna -a GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:27,756] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:27,757] [INFO] Task started: HMMsearch
[2024-01-25 18:42:27,757] [INFO] Running command: hmmsearch --tblout GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg453dfc2c-5ad2-410c-aace-88a4dfe77b77/dqc_reference/reference_markers.hmm GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:27,921] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:27,922] [INFO] Found 6/6 markers.
[2024-01-25 18:42:27,938] [INFO] Query marker FASTA was written to GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/markers.fasta
[2024-01-25 18:42:27,938] [INFO] Task started: Blastn
[2024-01-25 18:42:27,938] [INFO] Running command: blastn -query GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/markers.fasta -db /var/lib/cwl/stg453dfc2c-5ad2-410c-aace-88a4dfe77b77/dqc_reference/reference_markers.fasta -out GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:28,524] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:28,526] [INFO] Selected 12 target genomes.
[2024-01-25 18:42:28,527] [INFO] Target genome list was writen to GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/target_genomes.txt
[2024-01-25 18:42:28,532] [INFO] Task started: fastANI
[2024-01-25 18:42:28,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg323db889-1353-45a6-bced-19ee7347b10d/GCF_900155635.1_Olsenella_urinainfantis_genomic.fna.gz --refList GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/target_genomes.txt --output GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:34,867] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:34,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg453dfc2c-5ad2-410c-aace-88a4dfe77b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:34,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg453dfc2c-5ad2-410c-aace-88a4dfe77b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:34,875] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:34,876] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:34,876] [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
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	100.0	581	581	95	conclusive
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	81.4698	316	581	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	80.6501	256	581	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.3607	239	581	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	80.1537	275	581	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	80.1513	279	581	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.5802	233	581	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	78.8805	188	581	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	78.8445	176	581	95	below_threshold
Berryella wangjianweii	strain=zg-1050	GCA_013201155.1	2734634	2734634	type	True	77.8204	50	581	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:34,878] [INFO] DFAST Taxonomy check result was written to GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/tc_result.tsv
[2024-01-25 18:42:34,878] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:34,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:34,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg453dfc2c-5ad2-410c-aace-88a4dfe77b77/dqc_reference/checkm_data
[2024-01-25 18:42:34,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:34,899] [INFO] Task started: CheckM
[2024-01-25 18:42:34,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/checkm_input GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/checkm_result
[2024-01-25 18:42:53,749] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:53,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:53,766] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:53,766] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:53,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/markers.fasta)
[2024-01-25 18:42:53,766] [INFO] Task started: Blastn
[2024-01-25 18:42:53,766] [INFO] Running command: blastn -query GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/markers.fasta -db /var/lib/cwl/stg453dfc2c-5ad2-410c-aace-88a4dfe77b77/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:54,693] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:54,696] [INFO] Selected 15 target genomes.
[2024-01-25 18:42:54,696] [INFO] Target genome list was writen to GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:54,712] [INFO] Task started: fastANI
[2024-01-25 18:42:54,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg323db889-1353-45a6-bced-19ee7347b10d/GCF_900155635.1_Olsenella_urinainfantis_genomic.fna.gz --refList GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/target_genomes_gtdb.txt --output GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:01,344] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:01,355] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:01,356] [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_900155635.1	s__Olsenella_G urininfantis	100.0	581	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900120385.1	s__Olsenella_I phocaeensis	81.4697	316	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_I	95.0	97.88	97.64	0.87	0.85	3	-
GCF_001457795.1	s__Olsenella_F massiliensis	80.6567	255	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_F	95.0	98.66	97.33	0.97	0.93	3	-
GCF_003416765.1	s__Paratractidigestivibacter faecalis	80.3671	253	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.79	95.48	0.89	0.83	10	-
GCA_902780325.1	s__Parafannyhessea sp902787335	80.2273	197	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCF_000143845.1	s__Olsenella uli	80.173	277	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella	95.0	99.32	99.02	0.94	0.91	5	-
GCA_015062715.1	s__SIG37 sp015062715	80.1514	149	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__SIG37	95.0	96.94	96.94	0.73	0.73	2	-
GCA_905214865.1	s__Olsenella_H sp905214865	80.0417	242	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	99.90	99.90	0.96	0.96	2	-
GCF_009695875.1	s__Olsenella_H porci	79.9538	231	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	97.87	97.72	0.91	0.87	6	-
GCA_003862195.1	s__Parafannyhessea sp003862195	79.7563	245	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCA_900314575.1	s__UBA7741 sp900314575	79.5827	206	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	99.08	98.17	0.92	0.85	3	-
GCF_002160255.1	s__Thermophilibacter avistercoris	79.4825	253	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.79	97.22	0.93	0.92	5	-
GCA_902779675.1	s__UBA1367 sp902779675	79.0998	204	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.95	97.30	0.86	0.82	4	-
GCA_902788705.1	s__UBA1367 sp902788705	78.7799	202	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.66	97.66	0.87	0.87	2	-
GCA_902778135.1	s__UBA1367 sp902778135	78.7753	200	581	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.30	98.30	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:01,362] [INFO] GTDB search result was written to GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:01,362] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:01,366] [INFO] DFAST_QC result json was written to GCF_900155635.1_Olsenella_urinainfantis_genomic.fna/dqc_result.json
[2024-01-25 18:43:01,366] [INFO] DFAST_QC completed!
[2024-01-25 18:43:01,366] [INFO] Total running time: 0h0m40s