[2024-01-24 11:43:35,032] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:35,034] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:35,034] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a2c6525-e001-4a04-9222-b801011608af/dqc_reference
[2024-01-24 11:43:36,208] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:36,209] [INFO] Task started: Prodigal
[2024-01-24 11:43:36,209] [INFO] Running command: gunzip -c /var/lib/cwl/stg99ce732f-0aea-4343-9689-34d28a4a5e59/GCF_000214035.2_ASM21403v3_genomic.fna.gz | prodigal -d GCF_000214035.2_ASM21403v3_genomic.fna/cds.fna -a GCF_000214035.2_ASM21403v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:48,755] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:48,755] [INFO] Task started: HMMsearch
[2024-01-24 11:43:48,756] [INFO] Running command: hmmsearch --tblout GCF_000214035.2_ASM21403v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a2c6525-e001-4a04-9222-b801011608af/dqc_reference/reference_markers.hmm GCF_000214035.2_ASM21403v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:49,031] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:49,036] [INFO] Found 6/6 markers.
[2024-01-24 11:43:49,105] [INFO] Query marker FASTA was written to GCF_000214035.2_ASM21403v3_genomic.fna/markers.fasta
[2024-01-24 11:43:49,105] [INFO] Task started: Blastn
[2024-01-24 11:43:49,106] [INFO] Running command: blastn -query GCF_000214035.2_ASM21403v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a2c6525-e001-4a04-9222-b801011608af/dqc_reference/reference_markers.fasta -out GCF_000214035.2_ASM21403v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:50,116] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:50,120] [INFO] Selected 18 target genomes.
[2024-01-24 11:43:50,120] [INFO] Target genome list was writen to GCF_000214035.2_ASM21403v3_genomic.fna/target_genomes.txt
[2024-01-24 11:43:50,243] [INFO] Task started: fastANI
[2024-01-24 11:43:50,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ce732f-0aea-4343-9689-34d28a4a5e59/GCF_000214035.2_ASM21403v3_genomic.fna.gz --refList GCF_000214035.2_ASM21403v3_genomic.fna/target_genomes.txt --output GCF_000214035.2_ASM21403v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:07,058] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:07,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a2c6525-e001-4a04-9222-b801011608af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:07,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a2c6525-e001-4a04-9222-b801011608af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:07,077] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:07,077] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:07,077] [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 universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	100.0	1387	1390	95	conclusive
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	87.4354	1089	1390	95	below_threshold
Methyloversatilis thermotolerans	strain=3t	GCA_000372885.1	1346290	1346290	type	True	83.5661	911	1390	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.7861	456	1390	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	78.7076	363	1390	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.6162	452	1390	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	78.5417	396	1390	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	78.4915	478	1390	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	78.3775	396	1390	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.3491	418	1390	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	78.273	383	1390	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.1601	389	1390	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	78.0761	406	1390	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.0557	424	1390	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.8613	291	1390	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.3622	318	1390	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	77.2069	380	1390	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	77.1263	253	1390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:07,079] [INFO] DFAST Taxonomy check result was written to GCF_000214035.2_ASM21403v3_genomic.fna/tc_result.tsv
[2024-01-24 11:44:07,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:07,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:07,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a2c6525-e001-4a04-9222-b801011608af/dqc_reference/checkm_data
[2024-01-24 11:44:07,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:07,126] [INFO] Task started: CheckM
[2024-01-24 11:44:07,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000214035.2_ASM21403v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000214035.2_ASM21403v3_genomic.fna/checkm_input GCF_000214035.2_ASM21403v3_genomic.fna/checkm_result
[2024-01-24 11:44:52,946] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:52,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:52,969] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:52,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:52,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000214035.2_ASM21403v3_genomic.fna/markers.fasta)
[2024-01-24 11:44:52,970] [INFO] Task started: Blastn
[2024-01-24 11:44:52,971] [INFO] Running command: blastn -query GCF_000214035.2_ASM21403v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a2c6525-e001-4a04-9222-b801011608af/dqc_reference/reference_markers_gtdb.fasta -out GCF_000214035.2_ASM21403v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:54,929] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:54,933] [INFO] Selected 7 target genomes.
[2024-01-24 11:44:54,933] [INFO] Target genome list was writen to GCF_000214035.2_ASM21403v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:54,940] [INFO] Task started: fastANI
[2024-01-24 11:44:54,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ce732f-0aea-4343-9689-34d28a4a5e59/GCF_000214035.2_ASM21403v3_genomic.fna.gz --refList GCF_000214035.2_ASM21403v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000214035.2_ASM21403v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:03,166] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:03,178] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:03,178] [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_000214035.2	s__Methyloversatilis universalis	100.0	1387	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000378945.1	s__Methyloversatilis universalis_A	93.0232	1191	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527135.1	s__Methyloversatilis discipulorum	87.414	1091	1390	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	87.3801	1110	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	95.78	95.10	0.90	0.89	4	-
GCF_000372885.1	s__Methyloversatilis thermotolerans	83.5481	912	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791045.1	s__Methyloversatilis sp016791045	83.3557	810	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713355.1	s__Methyloversatilis sp001713355	83.1508	899	1390	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 11:45:03,180] [INFO] GTDB search result was written to GCF_000214035.2_ASM21403v3_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:03,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:03,187] [INFO] DFAST_QC result json was written to GCF_000214035.2_ASM21403v3_genomic.fna/dqc_result.json
[2024-01-24 11:45:03,187] [INFO] DFAST_QC completed!
[2024-01-24 11:45:03,187] [INFO] Total running time: 0h1m28s