[2024-01-24 12:14:33,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,740] [INFO] DQC Reference Directory: /var/lib/cwl/stge4a2485e-01e8-4c8e-9c7b-e38f4d492e18/dqc_reference
[2024-01-24 12:14:35,226] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,227] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,227] [INFO] Running command: gunzip -c /var/lib/cwl/stg14bdb074-fc8d-4faa-bd4a-dd2ff492da7b/GCF_008274945.1_ASM827494v1_genomic.fna.gz | prodigal -d GCF_008274945.1_ASM827494v1_genomic.fna/cds.fna -a GCF_008274945.1_ASM827494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:56,147] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:56,148] [INFO] Task started: HMMsearch
[2024-01-24 12:14:56,148] [INFO] Running command: hmmsearch --tblout GCF_008274945.1_ASM827494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4a2485e-01e8-4c8e-9c7b-e38f4d492e18/dqc_reference/reference_markers.hmm GCF_008274945.1_ASM827494v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:56,427] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:56,428] [INFO] Found 6/6 markers.
[2024-01-24 12:14:56,483] [INFO] Query marker FASTA was written to GCF_008274945.1_ASM827494v1_genomic.fna/markers.fasta
[2024-01-24 12:14:56,483] [INFO] Task started: Blastn
[2024-01-24 12:14:56,483] [INFO] Running command: blastn -query GCF_008274945.1_ASM827494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4a2485e-01e8-4c8e-9c7b-e38f4d492e18/dqc_reference/reference_markers.fasta -out GCF_008274945.1_ASM827494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:57,364] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:57,366] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:57,366] [INFO] Target genome list was writen to GCF_008274945.1_ASM827494v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:57,369] [INFO] Task started: fastANI
[2024-01-24 12:14:57,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg14bdb074-fc8d-4faa-bd4a-dd2ff492da7b/GCF_008274945.1_ASM827494v1_genomic.fna.gz --refList GCF_008274945.1_ASM827494v1_genomic.fna/target_genomes.txt --output GCF_008274945.1_ASM827494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:15,639] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:15,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4a2485e-01e8-4c8e-9c7b-e38f4d492e18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:15,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4a2485e-01e8-4c8e-9c7b-e38f4d492e18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:15,647] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:15:15,647] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:15,647] [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 brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	100.0	2327	2364	95	conclusive
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	99.9544	2246	2364	95	conclusive
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	99.9229	2170	2364	95	conclusive
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	99.9148	2058	2364	95	conclusive
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	94.9022	1592	2364	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	94.8959	2003	2364	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	93.9729	1794	2364	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	81.019	996	2364	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.9836	278	2364	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.2515	253	2364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:15,648] [INFO] DFAST Taxonomy check result was written to GCF_008274945.1_ASM827494v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:15,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:15,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:15,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4a2485e-01e8-4c8e-9c7b-e38f4d492e18/dqc_reference/checkm_data
[2024-01-24 12:15:15,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:15,717] [INFO] Task started: CheckM
[2024-01-24 12:15:15,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008274945.1_ASM827494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008274945.1_ASM827494v1_genomic.fna/checkm_input GCF_008274945.1_ASM827494v1_genomic.fna/checkm_result
[2024-01-24 12:16:32,933] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:32,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:32,951] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:32,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:32,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008274945.1_ASM827494v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:32,952] [INFO] Task started: Blastn
[2024-01-24 12:16:32,952] [INFO] Running command: blastn -query GCF_008274945.1_ASM827494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4a2485e-01e8-4c8e-9c7b-e38f4d492e18/dqc_reference/reference_markers_gtdb.fasta -out GCF_008274945.1_ASM827494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:34,573] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:34,576] [INFO] Selected 9 target genomes.
[2024-01-24 12:16:34,576] [INFO] Target genome list was writen to GCF_008274945.1_ASM827494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:34,580] [INFO] Task started: fastANI
[2024-01-24 12:16:34,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg14bdb074-fc8d-4faa-bd4a-dd2ff492da7b/GCF_008274945.1_ASM827494v1_genomic.fna.gz --refList GCF_008274945.1_ASM827494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008274945.1_ASM827494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:53,412] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:53,418] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:53,418] [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_001315015.1	s__Azospirillum brasilense	99.9156	2058	2364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	conclusive
GCF_003119195.2	s__Azospirillum baldaniorum	94.992	2049	2364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	97.20	95.48	0.90	0.83	11	-
GCF_003349955.1	s__Azospirillum brasilense_B	94.462	1866	2364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_003119115.1	s__Azospirillum sp003119115	94.4591	1993	2364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_008365405.1	s__Azospirillum brasilense_D	94.4357	1952	2364	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	94.3827	1965	2364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCF_007827795.1	s__Azospirillum brasilense_E	94.3776	1843	2364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCF_014192915.1	s__Azospirillum sp014192915	94.1782	1945	2364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245955.1	s__Azospirillum brasilense_A	93.9378	1926	2364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.48	97.48	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:53,420] [INFO] GTDB search result was written to GCF_008274945.1_ASM827494v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:53,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:53,422] [INFO] DFAST_QC result json was written to GCF_008274945.1_ASM827494v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:53,423] [INFO] DFAST_QC completed!
[2024-01-24 12:16:53,423] [INFO] Total running time: 0h2m20s