[2024-01-24 13:18:45,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:45,271] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:45,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg7018e611-38d1-461b-af12-76d7394d6d52/dqc_reference
[2024-01-24 13:18:46,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:46,648] [INFO] Task started: Prodigal
[2024-01-24 13:18:46,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fd033e2-4a1a-447d-8d88-c268c11714c1/GCF_009746125.1_ASM974612v1_genomic.fna.gz | prodigal -d GCF_009746125.1_ASM974612v1_genomic.fna/cds.fna -a GCF_009746125.1_ASM974612v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:02,728] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:02,728] [INFO] Task started: HMMsearch
[2024-01-24 13:19:02,728] [INFO] Running command: hmmsearch --tblout GCF_009746125.1_ASM974612v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7018e611-38d1-461b-af12-76d7394d6d52/dqc_reference/reference_markers.hmm GCF_009746125.1_ASM974612v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:03,008] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:03,009] [INFO] Found 6/6 markers.
[2024-01-24 13:19:03,047] [INFO] Query marker FASTA was written to GCF_009746125.1_ASM974612v1_genomic.fna/markers.fasta
[2024-01-24 13:19:03,047] [INFO] Task started: Blastn
[2024-01-24 13:19:03,047] [INFO] Running command: blastn -query GCF_009746125.1_ASM974612v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7018e611-38d1-461b-af12-76d7394d6d52/dqc_reference/reference_markers.fasta -out GCF_009746125.1_ASM974612v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:03,865] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:03,868] [INFO] Selected 24 target genomes.
[2024-01-24 13:19:03,868] [INFO] Target genome list was writen to GCF_009746125.1_ASM974612v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:03,884] [INFO] Task started: fastANI
[2024-01-24 13:19:03,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd033e2-4a1a-447d-8d88-c268c11714c1/GCF_009746125.1_ASM974612v1_genomic.fna.gz --refList GCF_009746125.1_ASM974612v1_genomic.fna/target_genomes.txt --output GCF_009746125.1_ASM974612v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:25,695] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:25,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7018e611-38d1-461b-af12-76d7394d6d52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:25,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7018e611-38d1-461b-af12-76d7394d6d52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:25,715] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:25,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:25,716] [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
Casimicrobium huifangae	strain=SJ-1	GCA_009746125.1	2591109	2591109	type	True	100.0	1487	1488	95	conclusive
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	77.5586	275	1488	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	77.1563	70	1488	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	77.1377	173	1488	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	77.1232	253	1488	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	77.1077	179	1488	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	76.9913	192	1488	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.9559	163	1488	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	76.8673	143	1488	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	76.7742	242	1488	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	76.7472	192	1488	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	76.7448	177	1488	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	76.7094	215	1488	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	76.6968	216	1488	95	below_threshold
Massilia polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	76.6606	141	1488	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	76.6556	244	1488	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	76.633	174	1488	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	76.6021	248	1488	95	below_threshold
Methyloversatilis thermotolerans	strain=3t	GCA_000372885.1	1346290	1346290	type	True	76.493	127	1488	95	below_threshold
Burkholderia seminalis	strain=LMG 24067	GCA_902832885.1	488731	488731	type	True	76.3738	185	1488	95	below_threshold
Burkholderia pseudomultivorans		GCA_902499075.1	1207504	1207504	suspected-type	True	76.3614	195	1488	95	below_threshold
Massilia horti	strain=ONC3	GCA_004614195.1	2562153	2562153	type	True	76.2806	160	1488	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	76.2335	185	1488	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	76.2209	187	1488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,723] [INFO] DFAST Taxonomy check result was written to GCF_009746125.1_ASM974612v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:25,725] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:25,725] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:25,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7018e611-38d1-461b-af12-76d7394d6d52/dqc_reference/checkm_data
[2024-01-24 13:19:25,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:25,778] [INFO] Task started: CheckM
[2024-01-24 13:19:25,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009746125.1_ASM974612v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009746125.1_ASM974612v1_genomic.fna/checkm_input GCF_009746125.1_ASM974612v1_genomic.fna/checkm_result
[2024-01-24 13:20:15,977] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:15,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:15,996] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:15,996] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:15,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009746125.1_ASM974612v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:15,996] [INFO] Task started: Blastn
[2024-01-24 13:20:15,997] [INFO] Running command: blastn -query GCF_009746125.1_ASM974612v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7018e611-38d1-461b-af12-76d7394d6d52/dqc_reference/reference_markers_gtdb.fasta -out GCF_009746125.1_ASM974612v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:17,248] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:17,251] [INFO] Selected 12 target genomes.
[2024-01-24 13:20:17,251] [INFO] Target genome list was writen to GCF_009746125.1_ASM974612v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:17,274] [INFO] Task started: fastANI
[2024-01-24 13:20:17,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd033e2-4a1a-447d-8d88-c268c11714c1/GCF_009746125.1_ASM974612v1_genomic.fna.gz --refList GCF_009746125.1_ASM974612v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009746125.1_ASM974612v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:26,550] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:26,560] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:26,560] [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_009746125.1	s__Casimicrobium huifangae	100.0	1486	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__Casimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016790165.1	s__Casimicrobium sp016790165	80.4596	663	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__Casimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241765.1	s__Casimicrobium sp018241765	79.2395	524	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__Casimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378555.1	s__Casimicrobium sp014378555	77.3379	303	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__Casimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017989135.1	s__Casimicrobium sp017989135	77.32	275	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__Casimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378945.1	s__Methyloversatilis universalis_A	77.1244	145	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722785.1	s__Ramlibacter monticola	77.0975	257	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716905.1	s__Acidovorax temperans	76.9586	144	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	96.32	95.61	0.84	0.79	8	-
GCA_004293675.1	s__Casimicrobium sp004293675	76.9176	199	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__Casimicrobium	95.0	97.20	97.20	0.87	0.87	2	-
GCA_013298045.1	s__Casimicrobium sp013298045	76.9121	207	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__Casimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298765.1	s__Casimicrobium sp013298765	76.7718	212	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__Casimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298455.1	s__Casimicrobium sp013298455	76.4988	177	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__Casimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:26,562] [INFO] GTDB search result was written to GCF_009746125.1_ASM974612v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:26,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:26,566] [INFO] DFAST_QC result json was written to GCF_009746125.1_ASM974612v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:26,566] [INFO] DFAST_QC completed!
[2024-01-24 13:20:26,566] [INFO] Total running time: 0h1m41s