[2024-01-24 13:28:44,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:44,548] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:44,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c9c1199-90c0-412d-a89d-7094a880b864/dqc_reference
[2024-01-24 13:28:45,833] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:45,834] [INFO] Task started: Prodigal
[2024-01-24 13:28:45,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c232908-593a-40bf-b748-59ede0faead7/GCF_000310185.1_ASM31018v1_genomic.fna.gz | prodigal -d GCF_000310185.1_ASM31018v1_genomic.fna/cds.fna -a GCF_000310185.1_ASM31018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:57,678] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:57,679] [INFO] Task started: HMMsearch
[2024-01-24 13:28:57,679] [INFO] Running command: hmmsearch --tblout GCF_000310185.1_ASM31018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c9c1199-90c0-412d-a89d-7094a880b864/dqc_reference/reference_markers.hmm GCF_000310185.1_ASM31018v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:57,981] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:57,982] [INFO] Found 6/6 markers.
[2024-01-24 13:28:58,025] [INFO] Query marker FASTA was written to GCF_000310185.1_ASM31018v1_genomic.fna/markers.fasta
[2024-01-24 13:28:58,025] [INFO] Task started: Blastn
[2024-01-24 13:28:58,025] [INFO] Running command: blastn -query GCF_000310185.1_ASM31018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c9c1199-90c0-412d-a89d-7094a880b864/dqc_reference/reference_markers.fasta -out GCF_000310185.1_ASM31018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:59,304] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:59,308] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:59,308] [INFO] Target genome list was writen to GCF_000310185.1_ASM31018v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:59,317] [INFO] Task started: fastANI
[2024-01-24 13:28:59,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c232908-593a-40bf-b748-59ede0faead7/GCF_000310185.1_ASM31018v1_genomic.fna.gz --refList GCF_000310185.1_ASM31018v1_genomic.fna/target_genomes.txt --output GCF_000310185.1_ASM31018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:14,933] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:14,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c9c1199-90c0-412d-a89d-7094a880b864/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:14,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c9c1199-90c0-412d-a89d-7094a880b864/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:14,945] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:14,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:14,946] [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
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	100.0	1264	1272	95	conclusive
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	91.9859	879	1272	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	84.6669	702	1272	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	84.6053	762	1272	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	84.5768	684	1272	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	84.4868	731	1272	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	84.3834	688	1272	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	84.1359	691	1272	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	83.4712	660	1272	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	83.4667	633	1272	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	80.9006	659	1272	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	80.0186	557	1272	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.9494	488	1272	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	79.7956	523	1272	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.4148	331	1272	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:14,949] [INFO] DFAST Taxonomy check result was written to GCF_000310185.1_ASM31018v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:14,950] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:14,950] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:14,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c9c1199-90c0-412d-a89d-7094a880b864/dqc_reference/checkm_data
[2024-01-24 13:29:14,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:14,995] [INFO] Task started: CheckM
[2024-01-24 13:29:14,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000310185.1_ASM31018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000310185.1_ASM31018v1_genomic.fna/checkm_input GCF_000310185.1_ASM31018v1_genomic.fna/checkm_result
[2024-01-24 13:29:57,297] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:57,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:57,405] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:57,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:57,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000310185.1_ASM31018v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:57,406] [INFO] Task started: Blastn
[2024-01-24 13:29:57,407] [INFO] Running command: blastn -query GCF_000310185.1_ASM31018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c9c1199-90c0-412d-a89d-7094a880b864/dqc_reference/reference_markers_gtdb.fasta -out GCF_000310185.1_ASM31018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:00,047] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:00,053] [INFO] Selected 8 target genomes.
[2024-01-24 13:30:00,053] [INFO] Target genome list was writen to GCF_000310185.1_ASM31018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:00,065] [INFO] Task started: fastANI
[2024-01-24 13:30:00,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c232908-593a-40bf-b748-59ede0faead7/GCF_000310185.1_ASM31018v1_genomic.fna.gz --refList GCF_000310185.1_ASM31018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000310185.1_ASM31018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:07,546] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:07,560] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:07,560] [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_000310185.1	s__Thauera aminoaromatica	100.0	1264	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	conclusive
GCF_000310225.1	s__Thauera phenylacetica	91.9993	877	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	91.9126	880	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790365.1	s__Thauera sp016790365	90.2862	653	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017997795.1	s__Thauera sp017997795	87.4466	572	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422685.1	s__Thauera sp002422685	86.8642	714	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	86.3789	598	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_009469595.1	s__Thauera sp009469595	83.4636	759	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:07,562] [INFO] GTDB search result was written to GCF_000310185.1_ASM31018v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:07,563] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:07,570] [INFO] DFAST_QC result json was written to GCF_000310185.1_ASM31018v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:07,571] [INFO] DFAST_QC completed!
[2024-01-24 13:30:07,571] [INFO] Total running time: 0h1m23s