[2024-01-24 12:13:52,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:52,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:52,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f4856bf-7410-4c5f-aa34-4e64cfd5a37d/dqc_reference
[2024-01-24 12:13:53,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:53,951] [INFO] Task started: Prodigal
[2024-01-24 12:13:53,951] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c27bd51-903f-431a-86ad-8bc0a1a975d5/GCF_000372885.1_ASM37288v1_genomic.fna.gz | prodigal -d GCF_000372885.1_ASM37288v1_genomic.fna/cds.fna -a GCF_000372885.1_ASM37288v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:08,779] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:08,780] [INFO] Task started: HMMsearch
[2024-01-24 12:14:08,780] [INFO] Running command: hmmsearch --tblout GCF_000372885.1_ASM37288v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f4856bf-7410-4c5f-aa34-4e64cfd5a37d/dqc_reference/reference_markers.hmm GCF_000372885.1_ASM37288v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:09,078] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:09,080] [INFO] Found 6/6 markers.
[2024-01-24 12:14:09,119] [INFO] Query marker FASTA was written to GCF_000372885.1_ASM37288v1_genomic.fna/markers.fasta
[2024-01-24 12:14:09,119] [INFO] Task started: Blastn
[2024-01-24 12:14:09,119] [INFO] Running command: blastn -query GCF_000372885.1_ASM37288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f4856bf-7410-4c5f-aa34-4e64cfd5a37d/dqc_reference/reference_markers.fasta -out GCF_000372885.1_ASM37288v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:10,051] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:10,054] [INFO] Selected 18 target genomes.
[2024-01-24 12:14:10,055] [INFO] Target genome list was writen to GCF_000372885.1_ASM37288v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:10,061] [INFO] Task started: fastANI
[2024-01-24 12:14:10,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c27bd51-903f-431a-86ad-8bc0a1a975d5/GCF_000372885.1_ASM37288v1_genomic.fna.gz --refList GCF_000372885.1_ASM37288v1_genomic.fna/target_genomes.txt --output GCF_000372885.1_ASM37288v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:25,284] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:25,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f4856bf-7410-4c5f-aa34-4e64cfd5a37d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:25,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f4856bf-7410-4c5f-aa34-4e64cfd5a37d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:25,305] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:25,305] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:25,305] [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
Methyloversatilis thermotolerans	strain=3t	GCA_000372885.1	1346290	1346290	type	True	100.0	1385	1385	95	conclusive
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	83.6207	954	1385	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	83.5302	903	1385	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.2221	360	1385	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	77.9835	302	1385	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	77.9424	305	1385	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	77.9321	314	1385	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.9137	298	1385	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	77.8622	280	1385	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	77.777	353	1385	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	77.4725	332	1385	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	77.334	331	1385	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	76.8218	194	1385	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	76.6947	321	1385	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	75.7583	160	1385	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.2269	133	1385	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.2196	92	1385	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	75.0055	60	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:25,307] [INFO] DFAST Taxonomy check result was written to GCF_000372885.1_ASM37288v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:25,308] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:25,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:25,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f4856bf-7410-4c5f-aa34-4e64cfd5a37d/dqc_reference/checkm_data
[2024-01-24 12:14:25,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:25,351] [INFO] Task started: CheckM
[2024-01-24 12:14:25,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000372885.1_ASM37288v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000372885.1_ASM37288v1_genomic.fna/checkm_input GCF_000372885.1_ASM37288v1_genomic.fna/checkm_result
[2024-01-24 12:15:34,718] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:34,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:34,745] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:34,745] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:34,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000372885.1_ASM37288v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:34,746] [INFO] Task started: Blastn
[2024-01-24 12:15:34,746] [INFO] Running command: blastn -query GCF_000372885.1_ASM37288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f4856bf-7410-4c5f-aa34-4e64cfd5a37d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000372885.1_ASM37288v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:36,583] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:36,588] [INFO] Selected 5 target genomes.
[2024-01-24 12:15:36,588] [INFO] Target genome list was writen to GCF_000372885.1_ASM37288v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:36,593] [INFO] Task started: fastANI
[2024-01-24 12:15:36,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c27bd51-903f-431a-86ad-8bc0a1a975d5/GCF_000372885.1_ASM37288v1_genomic.fna.gz --refList GCF_000372885.1_ASM37288v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000372885.1_ASM37288v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:42,190] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:42,199] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:42,199] [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_000372885.1	s__Methyloversatilis thermotolerans	100.0	1385	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000527135.1	s__Methyloversatilis discipulorum	83.6696	949	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	97.77	95.54	0.94	0.88	3	-
GCF_000385375.1	s__Methyloversatilis discipulorum_A	83.5962	962	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	95.78	95.10	0.90	0.89	4	-
GCF_000214035.2	s__Methyloversatilis universalis	83.4886	907	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000378945.1	s__Methyloversatilis universalis_A	83.4463	904	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:42,201] [INFO] GTDB search result was written to GCF_000372885.1_ASM37288v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:42,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:42,207] [INFO] DFAST_QC result json was written to GCF_000372885.1_ASM37288v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:42,207] [INFO] DFAST_QC completed!
[2024-01-24 12:15:42,208] [INFO] Total running time: 0h1m50s