[2023-06-13 17:24:48,412] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:24:48,413] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:24:48,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cc93f06-6094-42f4-a603-c827ba1eb4f9/dqc_reference
[2023-06-13 17:24:49,939] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:24:49,940] [INFO] Task started: Prodigal
[2023-06-13 17:24:49,940] [INFO] Running command: gunzip -c /var/lib/cwl/stg0172a82e-6169-416a-b8f9-738a24790aeb/GCA_022655095.1_ASM2265509v1_genomic.fna.gz | prodigal -d GCA_022655095.1_ASM2265509v1_genomic.fna/cds.fna -a GCA_022655095.1_ASM2265509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:24:55,293] [INFO] Task succeeded: Prodigal
[2023-06-13 17:24:55,294] [INFO] Task started: HMMsearch
[2023-06-13 17:24:55,294] [INFO] Running command: hmmsearch --tblout GCA_022655095.1_ASM2265509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cc93f06-6094-42f4-a603-c827ba1eb4f9/dqc_reference/reference_markers.hmm GCA_022655095.1_ASM2265509v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:24:55,441] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:24:55,442] [INFO] Found 6/6 markers.
[2023-06-13 17:24:55,461] [INFO] Query marker FASTA was written to GCA_022655095.1_ASM2265509v1_genomic.fna/markers.fasta
[2023-06-13 17:24:55,461] [INFO] Task started: Blastn
[2023-06-13 17:24:55,462] [INFO] Running command: blastn -query GCA_022655095.1_ASM2265509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc93f06-6094-42f4-a603-c827ba1eb4f9/dqc_reference/reference_markers.fasta -out GCA_022655095.1_ASM2265509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:24:56,051] [INFO] Task succeeded: Blastn
[2023-06-13 17:24:56,055] [INFO] Selected 17 target genomes.
[2023-06-13 17:24:56,055] [INFO] Target genome list was writen to GCA_022655095.1_ASM2265509v1_genomic.fna/target_genomes.txt
[2023-06-13 17:24:56,056] [INFO] Task started: fastANI
[2023-06-13 17:24:56,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg0172a82e-6169-416a-b8f9-738a24790aeb/GCA_022655095.1_ASM2265509v1_genomic.fna.gz --refList GCA_022655095.1_ASM2265509v1_genomic.fna/target_genomes.txt --output GCA_022655095.1_ASM2265509v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:25:03,570] [INFO] Task succeeded: fastANI
[2023-06-13 17:25:03,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cc93f06-6094-42f4-a603-c827ba1eb4f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:25:03,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cc93f06-6094-42f4-a603-c827ba1eb4f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:25:03,582] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:25:03,582] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:25:03,583] [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
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.7765	230	565	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.7075	220	565	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.5751	211	565	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	79.5177	186	565	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	79.513	207	565	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.3997	170	565	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	79.1882	155	565	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	79.085	147	565	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.0196	191	565	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	78.9044	194	565	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	78.3543	67	565	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	77.4533	85	565	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	77.3063	91	565	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	76.326	63	565	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:25:03,584] [INFO] DFAST Taxonomy check result was written to GCA_022655095.1_ASM2265509v1_genomic.fna/tc_result.tsv
[2023-06-13 17:25:03,585] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:25:03,585] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:25:03,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cc93f06-6094-42f4-a603-c827ba1eb4f9/dqc_reference/checkm_data
[2023-06-13 17:25:03,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:25:03,606] [INFO] Task started: CheckM
[2023-06-13 17:25:03,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022655095.1_ASM2265509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022655095.1_ASM2265509v1_genomic.fna/checkm_input GCA_022655095.1_ASM2265509v1_genomic.fna/checkm_result
[2023-06-13 17:25:24,424] [INFO] Task succeeded: CheckM
[2023-06-13 17:25:24,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:25:24,441] [INFO] ===== Completeness check finished =====
[2023-06-13 17:25:24,441] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:25:24,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022655095.1_ASM2265509v1_genomic.fna/markers.fasta)
[2023-06-13 17:25:24,441] [INFO] Task started: Blastn
[2023-06-13 17:25:24,442] [INFO] Running command: blastn -query GCA_022655095.1_ASM2265509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc93f06-6094-42f4-a603-c827ba1eb4f9/dqc_reference/reference_markers_gtdb.fasta -out GCA_022655095.1_ASM2265509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:25:25,318] [INFO] Task succeeded: Blastn
[2023-06-13 17:25:25,322] [INFO] Selected 10 target genomes.
[2023-06-13 17:25:25,322] [INFO] Target genome list was writen to GCA_022655095.1_ASM2265509v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:25:25,325] [INFO] Task started: fastANI
[2023-06-13 17:25:25,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg0172a82e-6169-416a-b8f9-738a24790aeb/GCA_022655095.1_ASM2265509v1_genomic.fna.gz --refList GCA_022655095.1_ASM2265509v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022655095.1_ASM2265509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:25:30,223] [INFO] Task succeeded: fastANI
[2023-06-13 17:25:30,232] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 17:25:30,232] [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_900548775.1	s__Tractidigestivibacter sp900548775	87.1563	399	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.69	98.21	0.83	0.74	10	-
GCF_900119625.1	s__Tractidigestivibacter sp900119625	87.0828	452	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	96.91	96.91	0.78	0.78	2	-
GCF_001494635.1	s__Tractidigestivibacter scatoligenes	86.9735	451	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000752675.2	s__Tractidigestivibacter sp000752675	86.9289	442	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.74	96.78	0.93	0.90	14	-
GCA_902834555.1	s__Tractidigestivibacter sp902834555	86.8788	444	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_902773995.1	s__Tractidigestivibacter sp902773995	86.7146	418	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.13	97.55	0.87	0.83	4	-
GCA_900768455.1	s__Tractidigestivibacter sp900768455	86.7072	379	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	97.35	97.35	0.93	0.93	2	-
GCF_900111695.1	s__Tractidigestivibacter sp900111695	86.6034	444	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770865.1	s__Tractidigestivibacter sp900770865	86.4203	311	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557505.1	s__Tractidigestivibacter sp004557505	85.2467	417	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 17:25:30,234] [INFO] GTDB search result was written to GCA_022655095.1_ASM2265509v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:25:30,235] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:25:30,238] [INFO] DFAST_QC result json was written to GCA_022655095.1_ASM2265509v1_genomic.fna/dqc_result.json
[2023-06-13 17:25:30,238] [INFO] DFAST_QC completed!
[2023-06-13 17:25:30,238] [INFO] Total running time: 0h0m42s