[2024-01-24 11:26:20,224] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,226] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,226] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe0aed07-0d91-4df7-8a5b-6af885d09905/dqc_reference
[2024-01-24 11:26:21,455] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:21,456] [INFO] Task started: Prodigal
[2024-01-24 11:26:21,456] [INFO] Running command: gunzip -c /var/lib/cwl/stg34cfddfe-8ce8-4a08-a079-715456d62ad9/GCF_016632405.1_ASM1663240v1_genomic.fna.gz | prodigal -d GCF_016632405.1_ASM1663240v1_genomic.fna/cds.fna -a GCF_016632405.1_ASM1663240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:41,910] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:41,911] [INFO] Task started: HMMsearch
[2024-01-24 11:26:41,911] [INFO] Running command: hmmsearch --tblout GCF_016632405.1_ASM1663240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe0aed07-0d91-4df7-8a5b-6af885d09905/dqc_reference/reference_markers.hmm GCF_016632405.1_ASM1663240v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:42,327] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:42,329] [INFO] Found 6/6 markers.
[2024-01-24 11:26:42,389] [INFO] Query marker FASTA was written to GCF_016632405.1_ASM1663240v1_genomic.fna/markers.fasta
[2024-01-24 11:26:42,390] [INFO] Task started: Blastn
[2024-01-24 11:26:42,390] [INFO] Running command: blastn -query GCF_016632405.1_ASM1663240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe0aed07-0d91-4df7-8a5b-6af885d09905/dqc_reference/reference_markers.fasta -out GCF_016632405.1_ASM1663240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:43,430] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:43,434] [INFO] Selected 12 target genomes.
[2024-01-24 11:26:43,434] [INFO] Target genome list was writen to GCF_016632405.1_ASM1663240v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:43,440] [INFO] Task started: fastANI
[2024-01-24 11:26:43,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg34cfddfe-8ce8-4a08-a079-715456d62ad9/GCF_016632405.1_ASM1663240v1_genomic.fna.gz --refList GCF_016632405.1_ASM1663240v1_genomic.fna/target_genomes.txt --output GCF_016632405.1_ASM1663240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:05,254] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:05,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe0aed07-0d91-4df7-8a5b-6af885d09905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:05,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe0aed07-0d91-4df7-8a5b-6af885d09905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:05,271] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:05,272] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:05,272] [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
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	94.4879	2006	2332	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	94.4822	1997	2332	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	94.3664	1875	2332	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	94.2903	1963	2332	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	94.2879	1958	2332	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	94.2781	1900	2332	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	94.2002	1777	2332	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	94.1959	1941	2332	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	94.1243	1544	2332	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	80.9618	986	2332	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.6318	516	2332	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.1497	247	2332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:05,273] [INFO] DFAST Taxonomy check result was written to GCF_016632405.1_ASM1663240v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:05,274] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:05,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:05,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe0aed07-0d91-4df7-8a5b-6af885d09905/dqc_reference/checkm_data
[2024-01-24 11:27:05,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:05,345] [INFO] Task started: CheckM
[2024-01-24 11:27:05,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016632405.1_ASM1663240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016632405.1_ASM1663240v1_genomic.fna/checkm_input GCF_016632405.1_ASM1663240v1_genomic.fna/checkm_result
[2024-01-24 11:28:09,980] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:09,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:10,005] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:10,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:10,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016632405.1_ASM1663240v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:10,006] [INFO] Task started: Blastn
[2024-01-24 11:28:10,006] [INFO] Running command: blastn -query GCF_016632405.1_ASM1663240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe0aed07-0d91-4df7-8a5b-6af885d09905/dqc_reference/reference_markers_gtdb.fasta -out GCF_016632405.1_ASM1663240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:11,996] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:12,001] [INFO] Selected 9 target genomes.
[2024-01-24 11:28:12,001] [INFO] Target genome list was writen to GCF_016632405.1_ASM1663240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:12,009] [INFO] Task started: fastANI
[2024-01-24 11:28:12,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg34cfddfe-8ce8-4a08-a079-715456d62ad9/GCF_016632405.1_ASM1663240v1_genomic.fna.gz --refList GCF_016632405.1_ASM1663240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016632405.1_ASM1663240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:30,949] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:30,963] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:30,963] [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_007827795.1	s__Azospirillum brasilense_E	98.9731	1906	2332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	conclusive
GCF_008365405.1	s__Azospirillum brasilense_D	94.726	1930	2332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119115.1	s__Azospirillum sp003119115	94.5662	1996	2332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_003119195.2	s__Azospirillum baldaniorum	94.4792	2007	2332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	97.20	95.48	0.90	0.83	11	-
GCF_001315015.1	s__Azospirillum brasilense	94.3785	1875	2332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
GCF_002245955.1	s__Azospirillum brasilense_A	94.1286	1896	2332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.48	97.48	0.91	0.91	2	-
GCF_003349955.1	s__Azospirillum brasilense_B	93.911	1864	2332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_014192915.1	s__Azospirillum sp014192915	93.8966	1913	2332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827815.1	s__Azospirillum brasilense_C	93.8329	1902	2332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:30,964] [INFO] GTDB search result was written to GCF_016632405.1_ASM1663240v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:30,965] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:30,969] [INFO] DFAST_QC result json was written to GCF_016632405.1_ASM1663240v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:30,969] [INFO] DFAST_QC completed!
[2024-01-24 11:28:30,969] [INFO] Total running time: 0h2m11s