[2024-01-25 19:10:35,422] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:35,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:35,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg54423c79-cbbb-4685-9e03-4da74819a4c1/dqc_reference
[2024-01-25 19:10:36,554] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:36,555] [INFO] Task started: Prodigal
[2024-01-25 19:10:36,555] [INFO] Running command: gunzip -c /var/lib/cwl/stg70ff7081-a158-4625-abcb-796b4b02e7db/GCF_000237365.1_ASM23736v1_genomic.fna.gz | prodigal -d GCF_000237365.1_ASM23736v1_genomic.fna/cds.fna -a GCF_000237365.1_ASM23736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:56,941] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:56,942] [INFO] Task started: HMMsearch
[2024-01-25 19:10:56,942] [INFO] Running command: hmmsearch --tblout GCF_000237365.1_ASM23736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54423c79-cbbb-4685-9e03-4da74819a4c1/dqc_reference/reference_markers.hmm GCF_000237365.1_ASM23736v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:57,300] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:57,301] [INFO] Found 6/6 markers.
[2024-01-25 19:10:57,357] [INFO] Query marker FASTA was written to GCF_000237365.1_ASM23736v1_genomic.fna/markers.fasta
[2024-01-25 19:10:57,357] [INFO] Task started: Blastn
[2024-01-25 19:10:57,357] [INFO] Running command: blastn -query GCF_000237365.1_ASM23736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54423c79-cbbb-4685-9e03-4da74819a4c1/dqc_reference/reference_markers.fasta -out GCF_000237365.1_ASM23736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:58,274] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:58,277] [INFO] Selected 11 target genomes.
[2024-01-25 19:10:58,277] [INFO] Target genome list was writen to GCF_000237365.1_ASM23736v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:58,285] [INFO] Task started: fastANI
[2024-01-25 19:10:58,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ff7081-a158-4625-abcb-796b4b02e7db/GCF_000237365.1_ASM23736v1_genomic.fna.gz --refList GCF_000237365.1_ASM23736v1_genomic.fna/target_genomes.txt --output GCF_000237365.1_ASM23736v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:19,550] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:19,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54423c79-cbbb-4685-9e03-4da74819a4c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:19,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54423c79-cbbb-4685-9e03-4da74819a4c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:19,559] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:11:19,559] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:11:19,559] [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_000237365.1	1064539	1064539	type	True	100.0	2505	2506	95	inconclusive
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	99.9534	2496	2506	95	inconclusive
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	95.7909	2148	2506	95	inconclusive
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	94.8892	2056	2506	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	94.8646	2049	2506	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	94.8343	1979	2506	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	94.586	1575	2506	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	94.2805	1841	2506	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	80.9966	999	2506	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	78.2429	718	2506	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.424	410	2506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:19,561] [INFO] DFAST Taxonomy check result was written to GCF_000237365.1_ASM23736v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:19,561] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:19,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:19,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54423c79-cbbb-4685-9e03-4da74819a4c1/dqc_reference/checkm_data
[2024-01-25 19:11:19,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:19,642] [INFO] Task started: CheckM
[2024-01-25 19:11:19,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000237365.1_ASM23736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000237365.1_ASM23736v1_genomic.fna/checkm_input GCF_000237365.1_ASM23736v1_genomic.fna/checkm_result
[2024-01-25 19:12:33,164] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:33,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:33,191] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:33,191] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:33,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000237365.1_ASM23736v1_genomic.fna/markers.fasta)
[2024-01-25 19:12:33,193] [INFO] Task started: Blastn
[2024-01-25 19:12:33,193] [INFO] Running command: blastn -query GCF_000237365.1_ASM23736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54423c79-cbbb-4685-9e03-4da74819a4c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000237365.1_ASM23736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:35,013] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:35,015] [INFO] Selected 8 target genomes.
[2024-01-25 19:12:35,016] [INFO] Target genome list was writen to GCF_000237365.1_ASM23736v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:35,022] [INFO] Task started: fastANI
[2024-01-25 19:12:35,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ff7081-a158-4625-abcb-796b4b02e7db/GCF_000237365.1_ASM23736v1_genomic.fna.gz --refList GCF_000237365.1_ASM23736v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000237365.1_ASM23736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:53,409] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:53,416] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:53,416] [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_003119195.2	s__Azospirillum baldaniorum	99.9534	2496	2506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	97.20	95.48	0.90	0.83	11	conclusive
GCF_001315015.1	s__Azospirillum brasilense	94.8713	1948	2506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
GCF_007827815.1	s__Azospirillum brasilense_C	94.7238	1987	2506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCF_008365405.1	s__Azospirillum brasilense_D	94.6037	1965	2506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192915.1	s__Azospirillum sp014192915	94.5649	1993	2506	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	94.5504	2070	2506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_003349955.1	s__Azospirillum brasilense_B	94.5434	1946	2506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_002245955.1	s__Azospirillum brasilense_A	94.2897	2017	2506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.48	97.48	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:53,418] [INFO] GTDB search result was written to GCF_000237365.1_ASM23736v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:53,420] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:53,422] [INFO] DFAST_QC result json was written to GCF_000237365.1_ASM23736v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:53,423] [INFO] DFAST_QC completed!
[2024-01-25 19:12:53,423] [INFO] Total running time: 0h2m18s