[2024-01-24 14:14:00,777] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:00,779] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:00,779] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e029b1a-202d-4311-b7eb-bd33eefdbdc6/dqc_reference
[2024-01-24 14:14:02,057] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:02,057] [INFO] Task started: Prodigal
[2024-01-24 14:14:02,058] [INFO] Running command: gunzip -c /var/lib/cwl/stg4721a5fa-8a08-4764-8ee7-0d357ac47fb4/GCF_001457795.1_Olsenella_massiliensis_genomic.fna.gz | prodigal -d GCF_001457795.1_Olsenella_massiliensis_genomic.fna/cds.fna -a GCF_001457795.1_Olsenella_massiliensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:07,969] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:07,969] [INFO] Task started: HMMsearch
[2024-01-24 14:14:07,969] [INFO] Running command: hmmsearch --tblout GCF_001457795.1_Olsenella_massiliensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e029b1a-202d-4311-b7eb-bd33eefdbdc6/dqc_reference/reference_markers.hmm GCF_001457795.1_Olsenella_massiliensis_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:08,263] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:08,264] [INFO] Found 6/6 markers.
[2024-01-24 14:14:08,290] [INFO] Query marker FASTA was written to GCF_001457795.1_Olsenella_massiliensis_genomic.fna/markers.fasta
[2024-01-24 14:14:08,291] [INFO] Task started: Blastn
[2024-01-24 14:14:08,291] [INFO] Running command: blastn -query GCF_001457795.1_Olsenella_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e029b1a-202d-4311-b7eb-bd33eefdbdc6/dqc_reference/reference_markers.fasta -out GCF_001457795.1_Olsenella_massiliensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:09,402] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:09,405] [INFO] Selected 11 target genomes.
[2024-01-24 14:14:09,405] [INFO] Target genome list was writen to GCF_001457795.1_Olsenella_massiliensis_genomic.fna/target_genomes.txt
[2024-01-24 14:14:09,465] [INFO] Task started: fastANI
[2024-01-24 14:14:09,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg4721a5fa-8a08-4764-8ee7-0d357ac47fb4/GCF_001457795.1_Olsenella_massiliensis_genomic.fna.gz --refList GCF_001457795.1_Olsenella_massiliensis_genomic.fna/target_genomes.txt --output GCF_001457795.1_Olsenella_massiliensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:16,945] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:16,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e029b1a-202d-4311-b7eb-bd33eefdbdc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:16,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e029b1a-202d-4311-b7eb-bd33eefdbdc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:16,956] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:16,956] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:16,957] [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 massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	100.0	601	601	95	conclusive
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	80.6227	287	601	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	80.3941	271	601	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.2235	252	601	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	80.0885	243	601	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	80.0508	239	601	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.3381	249	601	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.3234	251	601	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	79.1698	228	601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:16,967] [INFO] DFAST Taxonomy check result was written to GCF_001457795.1_Olsenella_massiliensis_genomic.fna/tc_result.tsv
[2024-01-24 14:14:16,968] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:16,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:16,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e029b1a-202d-4311-b7eb-bd33eefdbdc6/dqc_reference/checkm_data
[2024-01-24 14:14:16,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:17,005] [INFO] Task started: CheckM
[2024-01-24 14:14:17,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001457795.1_Olsenella_massiliensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001457795.1_Olsenella_massiliensis_genomic.fna/checkm_input GCF_001457795.1_Olsenella_massiliensis_genomic.fna/checkm_result
[2024-01-24 14:14:43,073] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:43,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:43,096] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:43,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:43,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001457795.1_Olsenella_massiliensis_genomic.fna/markers.fasta)
[2024-01-24 14:14:43,097] [INFO] Task started: Blastn
[2024-01-24 14:14:43,097] [INFO] Running command: blastn -query GCF_001457795.1_Olsenella_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e029b1a-202d-4311-b7eb-bd33eefdbdc6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001457795.1_Olsenella_massiliensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:44,305] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:44,308] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:44,308] [INFO] Target genome list was writen to GCF_001457795.1_Olsenella_massiliensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:44,374] [INFO] Task started: fastANI
[2024-01-24 14:14:44,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg4721a5fa-8a08-4764-8ee7-0d357ac47fb4/GCF_001457795.1_Olsenella_massiliensis_genomic.fna.gz --refList GCF_001457795.1_Olsenella_massiliensis_genomic.fna/target_genomes_gtdb.txt --output GCF_001457795.1_Olsenella_massiliensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:52,133] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:52,164] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:52,165] [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_001457795.1	s__Olsenella_F massiliensis	100.0	601	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_F	95.0	98.66	97.33	0.97	0.93	3	conclusive
GCF_900120385.1	s__Olsenella_I phocaeensis	80.6153	288	601	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_000468755.1	s__Olsenella_F profusa_A	80.445	273	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155635.1	s__Olsenella_G urininfantis	80.3941	271	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780325.1	s__Parafannyhessea sp902787335	80.2993	196	601	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	80.0885	243	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella	95.0	99.32	99.02	0.94	0.91	5	-
GCF_014982725.1	s__Thermophilibacter sp014982725	79.8392	225	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314575.1	s__UBA7741 sp900314575	79.7908	216	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	99.08	98.17	0.92	0.85	3	-
GCF_900105025.1	s__Parafannyhessea umbonata	79.7513	238	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	95.62	95.16	0.88	0.79	34	-
GCA_905214865.1	s__Olsenella_H sp905214865	79.6289	258	601	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_016900315.1	s__Thermophilibacter profusa_A	79.4526	234	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159495.1	s__Thermophilibacter sp002159495	79.4281	252	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159535.1	s__Thermophilibacter sp002159535	79.4275	233	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416765.1	s__Paratractidigestivibacter faecalis	79.3859	242	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.79	95.48	0.89	0.83	10	-
GCA_902779675.1	s__UBA1367 sp902779675	79.2898	212	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.95	97.30	0.86	0.82	4	-
GCA_900316105.1	s__Olsenella_F sp900316105	79.2605	236	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_F	95.0	99.68	99.68	0.95	0.93	3	-
GCA_017941585.1	s__Parafannyhessea sp017941585	79.0704	173	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:52,167] [INFO] GTDB search result was written to GCF_001457795.1_Olsenella_massiliensis_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:52,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:52,173] [INFO] DFAST_QC result json was written to GCF_001457795.1_Olsenella_massiliensis_genomic.fna/dqc_result.json
[2024-01-24 14:14:52,173] [INFO] DFAST_QC completed!
[2024-01-24 14:14:52,173] [INFO] Total running time: 0h0m51s