[2024-01-25 18:41:05,682] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:05,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:05,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c74102b-ae84-4fab-844c-4f5bf09de905/dqc_reference
[2024-01-25 18:41:06,827] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:06,828] [INFO] Task started: Prodigal
[2024-01-25 18:41:06,828] [INFO] Running command: gunzip -c /var/lib/cwl/stg75b854ee-3331-4ad9-a3a1-be4ca18f8f07/GCF_002252525.1_ASM225252v1_genomic.fna.gz | prodigal -d GCF_002252525.1_ASM225252v1_genomic.fna/cds.fna -a GCF_002252525.1_ASM225252v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:21,467] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:21,468] [INFO] Task started: HMMsearch
[2024-01-25 18:41:21,468] [INFO] Running command: hmmsearch --tblout GCF_002252525.1_ASM225252v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c74102b-ae84-4fab-844c-4f5bf09de905/dqc_reference/reference_markers.hmm GCF_002252525.1_ASM225252v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:21,778] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:21,780] [INFO] Found 6/6 markers.
[2024-01-25 18:41:21,846] [INFO] Query marker FASTA was written to GCF_002252525.1_ASM225252v1_genomic.fna/markers.fasta
[2024-01-25 18:41:21,846] [INFO] Task started: Blastn
[2024-01-25 18:41:21,846] [INFO] Running command: blastn -query GCF_002252525.1_ASM225252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c74102b-ae84-4fab-844c-4f5bf09de905/dqc_reference/reference_markers.fasta -out GCF_002252525.1_ASM225252v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:22,535] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:22,538] [INFO] Selected 14 target genomes.
[2024-01-25 18:41:22,538] [INFO] Target genome list was writen to GCF_002252525.1_ASM225252v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:22,546] [INFO] Task started: fastANI
[2024-01-25 18:41:22,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg75b854ee-3331-4ad9-a3a1-be4ca18f8f07/GCF_002252525.1_ASM225252v1_genomic.fna.gz --refList GCF_002252525.1_ASM225252v1_genomic.fna/target_genomes.txt --output GCF_002252525.1_ASM225252v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:35,992] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:35,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c74102b-ae84-4fab-844c-4f5bf09de905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:35,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c74102b-ae84-4fab-844c-4f5bf09de905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:36,001] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:41:36,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:36,002] [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
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	100.0	1817	1822	95	conclusive
Brucella pituitosa	strain=CCUG 50899	GCA_003049685.2	571256	571256	type	True	85.8293	1223	1822	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_008801705.1	571256	571256	type	True	85.748	1207	1822	95	below_threshold
Brucella grignonensis	strain=OgA9a	GCA_002252505.1	94627	94627	type	True	85.5623	1081	1822	95	below_threshold
[Ochrobactrum] quorumnocens	strain=A44	GCA_002278035.1	271865	271865	type	True	84.4669	1199	1822	95	below_threshold
Brucella thiophenivorans	strain=DSM 7216	GCA_002252445.1	571255	571255	type	True	83.8684	942	1822	95	below_threshold
Brucella rhizosphaerae	strain=PR17	GCA_002252475.1	571254	571254	type	True	83.7274	1150	1822	95	below_threshold
Brucella gallinifaecis	strain=ISO 196	GCA_006476605.1	215590	215590	type	True	83.0403	806	1822	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	78.1687	288	1822	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	78.1429	290	1822	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	76.573	72	1822	95	below_threshold
Notoacmeibacter marinus	strain=XMTR2A4	GCA_002238045.1	1876515	1876515	type	True	76.3684	100	1822	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	75.7148	64	1822	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:36,003] [INFO] DFAST Taxonomy check result was written to GCF_002252525.1_ASM225252v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:36,005] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:36,006] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:36,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c74102b-ae84-4fab-844c-4f5bf09de905/dqc_reference/checkm_data
[2024-01-25 18:41:36,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:36,056] [INFO] Task started: CheckM
[2024-01-25 18:41:36,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002252525.1_ASM225252v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002252525.1_ASM225252v1_genomic.fna/checkm_input GCF_002252525.1_ASM225252v1_genomic.fna/checkm_result
[2024-01-25 18:42:19,857] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:19,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:19,877] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:19,878] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:19,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002252525.1_ASM225252v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:19,879] [INFO] Task started: Blastn
[2024-01-25 18:42:19,879] [INFO] Running command: blastn -query GCF_002252525.1_ASM225252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c74102b-ae84-4fab-844c-4f5bf09de905/dqc_reference/reference_markers_gtdb.fasta -out GCF_002252525.1_ASM225252v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:21,033] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:21,036] [INFO] Selected 9 target genomes.
[2024-01-25 18:42:21,036] [INFO] Target genome list was writen to GCF_002252525.1_ASM225252v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:21,044] [INFO] Task started: fastANI
[2024-01-25 18:42:21,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg75b854ee-3331-4ad9-a3a1-be4ca18f8f07/GCF_002252525.1_ASM225252v1_genomic.fna.gz --refList GCF_002252525.1_ASM225252v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002252525.1_ASM225252v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:32,105] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:32,111] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:32,112] [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_002252525.1	s__Ochrobactrum_A pseudogrignonensis	100.0	1817	1822	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	conclusive
GCF_018798825.1	s__Ochrobactrum_A sp018798825	94.566	1302	1822	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_014397025.1	s__Ochrobactrum_A sp014397025	87.4233	1040	1822	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	85.8386	1221	1822	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_002252505.1	s__Ochrobactrum_A grignonensis	85.5519	1082	1822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	99.78	99.78	1.00	1.00	2	-
GCF_002278035.1	s__Ochrobactrum_A quorumnocens	84.4858	1197	1822	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_002252445.1	s__Ochrobactrum_A thiophenivorans	83.8569	943	1822	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_002252475.1	s__Ochrobactrum_A rhizosphaerae	83.7381	1148	1822	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_006476605.1	s__Ochrobactrum_A gallinifaecis	83.0403	806	1822	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	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:32,113] [INFO] GTDB search result was written to GCF_002252525.1_ASM225252v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:32,114] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:32,117] [INFO] DFAST_QC result json was written to GCF_002252525.1_ASM225252v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:32,117] [INFO] DFAST_QC completed!
[2024-01-25 18:42:32,117] [INFO] Total running time: 0h1m26s