[2024-01-24 11:27:04,678] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,680] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ba8379e-6c94-4544-8576-85fc80fcbc10/dqc_reference
[2024-01-24 11:27:05,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,928] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,928] [INFO] Running command: gunzip -c /var/lib/cwl/stg8711f8db-5e50-41a9-8e50-8e96a4a3f576/GCF_003259955.1_ASM325995v1_genomic.fna.gz | prodigal -d GCF_003259955.1_ASM325995v1_genomic.fna/cds.fna -a GCF_003259955.1_ASM325995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:15,102] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:15,103] [INFO] Task started: HMMsearch
[2024-01-24 11:27:15,103] [INFO] Running command: hmmsearch --tblout GCF_003259955.1_ASM325995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ba8379e-6c94-4544-8576-85fc80fcbc10/dqc_reference/reference_markers.hmm GCF_003259955.1_ASM325995v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:15,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:15,372] [INFO] Found 6/6 markers.
[2024-01-24 11:27:15,404] [INFO] Query marker FASTA was written to GCF_003259955.1_ASM325995v1_genomic.fna/markers.fasta
[2024-01-24 11:27:15,405] [INFO] Task started: Blastn
[2024-01-24 11:27:15,405] [INFO] Running command: blastn -query GCF_003259955.1_ASM325995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ba8379e-6c94-4544-8576-85fc80fcbc10/dqc_reference/reference_markers.fasta -out GCF_003259955.1_ASM325995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:16,051] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:16,055] [INFO] Selected 21 target genomes.
[2024-01-24 11:27:16,055] [INFO] Target genome list was writen to GCF_003259955.1_ASM325995v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:16,098] [INFO] Task started: fastANI
[2024-01-24 11:27:16,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg8711f8db-5e50-41a9-8e50-8e96a4a3f576/GCF_003259955.1_ASM325995v1_genomic.fna.gz --refList GCF_003259955.1_ASM325995v1_genomic.fna/target_genomes.txt --output GCF_003259955.1_ASM325995v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:30,638] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:30,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ba8379e-6c94-4544-8576-85fc80fcbc10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:30,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ba8379e-6c94-4544-8576-85fc80fcbc10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:30,658] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:30,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:30,658] [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
Falsochrobactrum ovis	strain=DSM 26720	GCA_003259955.1	1293442	1293442	type	True	100.0	1071	1071	95	conclusive
Brucella gallinifaecis	strain=ISO 196	GCA_006476605.1	215590	215590	type	True	78.5138	324	1071	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_003049685.2	571256	571256	type	True	78.4059	332	1071	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_008801705.1	571256	571256	type	True	78.3955	333	1071	95	below_threshold
[Ochrobactrum] quorumnocens	strain=A44	GCA_002278035.1	271865	271865	type	True	78.3282	330	1071	95	below_threshold
Brucella melitensis	strain=16M	GCA_000160295.1	29459	29459	suspected-type	True	78.2095	278	1071	95	below_threshold
Brucella grignonensis	strain=OgA9a	GCA_002252505.1	94627	94627	type	True	78.1952	338	1071	95	below_threshold
Brucella haematophila	strain=CCUG 38531	GCA_005938105.1	419474	419474	type	True	78.1931	303	1071	95	below_threshold
Brucella rhizosphaerae	strain=PR17	GCA_002252475.1	571254	571254	type	True	78.1623	324	1071	95	below_threshold
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	78.1604	325	1071	95	below_threshold
Brucella thiophenivorans	strain=DSM 7216	GCA_002252445.1	571255	571255	type	True	78.0559	337	1071	95	below_threshold
Brucella daejeonensis	strain=DSM 26944	GCA_014199265.1	659015	659015	type	True	77.9691	279	1071	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	77.6359	163	1071	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.6359	163	1071	95	below_threshold
Phyllobacterium pellucidum	strain=BT25	GCA_013327855.1	2740464	2740464	type	True	76.8856	77	1071	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.5782	67	1071	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	76.4043	72	1071	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.9424	60	1071	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:30,660] [INFO] DFAST Taxonomy check result was written to GCF_003259955.1_ASM325995v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:30,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:30,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:30,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ba8379e-6c94-4544-8576-85fc80fcbc10/dqc_reference/checkm_data
[2024-01-24 11:27:30,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:30,693] [INFO] Task started: CheckM
[2024-01-24 11:27:30,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259955.1_ASM325995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259955.1_ASM325995v1_genomic.fna/checkm_input GCF_003259955.1_ASM325995v1_genomic.fna/checkm_result
[2024-01-24 11:28:02,617] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:02,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:02,635] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:02,636] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:02,636] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259955.1_ASM325995v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:02,637] [INFO] Task started: Blastn
[2024-01-24 11:28:02,637] [INFO] Running command: blastn -query GCF_003259955.1_ASM325995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ba8379e-6c94-4544-8576-85fc80fcbc10/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259955.1_ASM325995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:03,585] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:03,589] [INFO] Selected 18 target genomes.
[2024-01-24 11:28:03,589] [INFO] Target genome list was writen to GCF_003259955.1_ASM325995v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:03,612] [INFO] Task started: fastANI
[2024-01-24 11:28:03,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg8711f8db-5e50-41a9-8e50-8e96a4a3f576/GCF_003259955.1_ASM325995v1_genomic.fna.gz --refList GCF_003259955.1_ASM325995v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259955.1_ASM325995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:16,970] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:16,987] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:16,987] [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_003259955.1	s__Falsochrobactrum ovis	100.0	1071	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Falsochrobactrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003149535.1	s__Falsochrobactrum shanghaiense	78.8829	424	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Falsochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019100495.1	s__Falsochrobactrum sp019100495	78.5598	412	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Falsochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006476605.1	s__Ochrobactrum_A gallinifaecis	78.5138	324	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049685.1	s__Ochrobactrum_A pituitosa	78.4257	329	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	98.27	97.05	0.91	0.82	14	-
GCF_002278035.1	s__Ochrobactrum_A quorumnocens	78.3829	330	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	97.19	96.78	0.85	0.82	5	-
GCF_004368705.1	s__Ochrobactrum_A sp004368705	78.2459	321	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018798825.1	s__Ochrobactrum_A sp018798825	78.2331	325	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550135.1	s__Ochrobactrum_B haematophila_B	78.2218	303	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938105.1	s__Ochrobactrum_B haematophila	78.1914	302	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	98.61	97.38	0.92	0.84	3	-
GCF_002252475.1	s__Ochrobactrum_A rhizosphaerae	78.1623	324	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252525.1	s__Ochrobactrum_A pseudogrignonensis	78.1604	325	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	97.50	96.15	0.90	0.81	34	-
GCF_002252445.1	s__Ochrobactrum_A thiophenivorans	78.0559	337	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138095.1	s__Ochrobactrum_B sp014138095	78.0408	297	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013327855.1	s__Phyllobacterium pellucidum	76.8856	77	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	97.81	96.22	0.94	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:16,989] [INFO] GTDB search result was written to GCF_003259955.1_ASM325995v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:16,989] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:16,996] [INFO] DFAST_QC result json was written to GCF_003259955.1_ASM325995v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:16,996] [INFO] DFAST_QC completed!
[2024-01-24 11:28:16,996] [INFO] Total running time: 0h1m12s