[2024-01-24 13:22:10,292] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,295] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg9672268e-a048-4d1f-873b-c13d8472032f/dqc_reference
[2024-01-24 13:22:11,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:11,635] [INFO] Task started: Prodigal
[2024-01-24 13:22:11,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg742b9bbc-5fd5-47ba-a960-7f3b8a4ead71/GCF_003314995.1_ASM331499v1_genomic.fna.gz | prodigal -d GCF_003314995.1_ASM331499v1_genomic.fna/cds.fna -a GCF_003314995.1_ASM331499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:25,680] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:25,681] [INFO] Task started: HMMsearch
[2024-01-24 13:22:25,681] [INFO] Running command: hmmsearch --tblout GCF_003314995.1_ASM331499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9672268e-a048-4d1f-873b-c13d8472032f/dqc_reference/reference_markers.hmm GCF_003314995.1_ASM331499v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:25,991] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:25,993] [INFO] Found 6/6 markers.
[2024-01-24 13:22:26,037] [INFO] Query marker FASTA was written to GCF_003314995.1_ASM331499v1_genomic.fna/markers.fasta
[2024-01-24 13:22:26,038] [INFO] Task started: Blastn
[2024-01-24 13:22:26,038] [INFO] Running command: blastn -query GCF_003314995.1_ASM331499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9672268e-a048-4d1f-873b-c13d8472032f/dqc_reference/reference_markers.fasta -out GCF_003314995.1_ASM331499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:26,804] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:26,807] [INFO] Selected 8 target genomes.
[2024-01-24 13:22:26,808] [INFO] Target genome list was writen to GCF_003314995.1_ASM331499v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:26,815] [INFO] Task started: fastANI
[2024-01-24 13:22:26,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg742b9bbc-5fd5-47ba-a960-7f3b8a4ead71/GCF_003314995.1_ASM331499v1_genomic.fna.gz --refList GCF_003314995.1_ASM331499v1_genomic.fna/target_genomes.txt --output GCF_003314995.1_ASM331499v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:35,213] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:35,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9672268e-a048-4d1f-873b-c13d8472032f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:35,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9672268e-a048-4d1f-873b-c13d8472032f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:35,222] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:35,222] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:35,223] [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
Pseudochrobactrum asaccharolyticum	strain=DSM 25619	GCA_003314995.1	354351	354351	type	True	100.0	1525	1527	95	conclusive
Pseudochrobactrum saccharolyticum	strain=CCUG 33852	GCA_008801715.1	354352	354352	type	True	86.9385	1003	1527	95	below_threshold
Pseudochrobactrum saccharolyticum	strain=DSM 25620	GCA_014203195.1	354352	354352	type	True	86.8821	1012	1527	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	86.8458	1032	1527	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	86.8453	1032	1527	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	76.8459	117	1527	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.5923	129	1527	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	76.2261	82	1527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:35,224] [INFO] DFAST Taxonomy check result was written to GCF_003314995.1_ASM331499v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:35,225] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:35,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:35,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9672268e-a048-4d1f-873b-c13d8472032f/dqc_reference/checkm_data
[2024-01-24 13:22:35,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:35,272] [INFO] Task started: CheckM
[2024-01-24 13:22:35,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003314995.1_ASM331499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003314995.1_ASM331499v1_genomic.fna/checkm_input GCF_003314995.1_ASM331499v1_genomic.fna/checkm_result
[2024-01-24 13:23:19,966] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:19,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:19,982] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:19,983] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:19,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003314995.1_ASM331499v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:19,984] [INFO] Task started: Blastn
[2024-01-24 13:23:19,984] [INFO] Running command: blastn -query GCF_003314995.1_ASM331499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9672268e-a048-4d1f-873b-c13d8472032f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003314995.1_ASM331499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:20,948] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:20,952] [INFO] Selected 13 target genomes.
[2024-01-24 13:23:20,952] [INFO] Target genome list was writen to GCF_003314995.1_ASM331499v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:20,974] [INFO] Task started: fastANI
[2024-01-24 13:23:20,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg742b9bbc-5fd5-47ba-a960-7f3b8a4ead71/GCF_003314995.1_ASM331499v1_genomic.fna.gz --refList GCF_003314995.1_ASM331499v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003314995.1_ASM331499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:32,040] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:32,051] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:32,051] [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_003314995.1	s__Pseudochrobactrum asaccharolyticum	100.0	1525	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum	95.0	95.18	95.14	0.85	0.85	3	conclusive
GCA_900470285.1	s__Pseudochrobactrum sp900470285	87.6625	1015	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum	95.0	97.83	97.83	0.89	0.89	2	-
GCF_008801715.1	s__Pseudochrobactrum saccharolyticum	86.9385	1003	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum	95.0	96.83	96.24	0.94	0.92	10	-
GCF_014205685.1	s__Paenochrobactrum gallinarii	79.1023	358	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paenochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018798825.1	s__Ochrobactrum_A sp018798825	78.1609	293	1527	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	78.1178	259	1527	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	78.1059	308	1527	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_003049685.1	s__Ochrobactrum_A pituitosa	78.068	286	1527	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_014397025.1	s__Ochrobactrum_A sp014397025	77.8502	248	1527	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_000017405.1	s__Ochrobactrum anthropi	77.7494	274	1527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.518	98.11	96.94	0.89	0.83	55	-
GCF_002278035.1	s__Ochrobactrum_A quorumnocens	77.6814	273	1527	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_002252475.1	s__Ochrobactrum_A rhizosphaerae	77.5794	262	1527	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_013327855.1	s__Phyllobacterium pellucidum	76.3276	108	1527	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 13:23:32,053] [INFO] GTDB search result was written to GCF_003314995.1_ASM331499v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:32,053] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:32,056] [INFO] DFAST_QC result json was written to GCF_003314995.1_ASM331499v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:32,057] [INFO] DFAST_QC completed!
[2024-01-24 13:23:32,057] [INFO] Total running time: 0h1m22s