[2024-01-24 14:30:16,037] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:16,039] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:16,039] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f0cf6fb-0467-4906-ac35-51f3fcc5a41a/dqc_reference
[2024-01-24 14:30:17,372] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:17,373] [INFO] Task started: Prodigal
[2024-01-24 14:30:17,373] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e7e0d8d-490f-429a-9d2a-c3176152fc80/GCF_014205765.1_ASM1420576v1_genomic.fna.gz | prodigal -d GCF_014205765.1_ASM1420576v1_genomic.fna/cds.fna -a GCF_014205765.1_ASM1420576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:40,615] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:40,615] [INFO] Task started: HMMsearch
[2024-01-24 14:30:40,615] [INFO] Running command: hmmsearch --tblout GCF_014205765.1_ASM1420576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f0cf6fb-0467-4906-ac35-51f3fcc5a41a/dqc_reference/reference_markers.hmm GCF_014205765.1_ASM1420576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:40,967] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:40,969] [INFO] Found 6/6 markers.
[2024-01-24 14:30:41,028] [INFO] Query marker FASTA was written to GCF_014205765.1_ASM1420576v1_genomic.fna/markers.fasta
[2024-01-24 14:30:41,028] [INFO] Task started: Blastn
[2024-01-24 14:30:41,028] [INFO] Running command: blastn -query GCF_014205765.1_ASM1420576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f0cf6fb-0467-4906-ac35-51f3fcc5a41a/dqc_reference/reference_markers.fasta -out GCF_014205765.1_ASM1420576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:42,045] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:42,049] [INFO] Selected 23 target genomes.
[2024-01-24 14:30:42,049] [INFO] Target genome list was writen to GCF_014205765.1_ASM1420576v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:42,059] [INFO] Task started: fastANI
[2024-01-24 14:30:42,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e7e0d8d-490f-429a-9d2a-c3176152fc80/GCF_014205765.1_ASM1420576v1_genomic.fna.gz --refList GCF_014205765.1_ASM1420576v1_genomic.fna/target_genomes.txt --output GCF_014205765.1_ASM1420576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:10,827] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:10,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f0cf6fb-0467-4906-ac35-51f3fcc5a41a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:10,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f0cf6fb-0467-4906-ac35-51f3fcc5a41a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:10,845] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:10,845] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:10,845] [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
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	100.0	2340	2341	95	conclusive
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	78.0061	476	2341	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	77.9994	621	2341	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	77.9824	528	2341	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	77.9576	556	2341	95	below_threshold
Niveispirillum cyanobacteriorum	strain=TH16	GCA_002868735.1	1612173	1612173	type	True	77.9006	510	2341	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	77.8906	579	2341	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	77.868	587	2341	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	77.8582	574	2341	95	below_threshold
Niveispirillum cyanobacteriorum	strain=CGMCC 1.12958	GCA_014640215.1	1612173	1612173	type	True	77.8515	505	2341	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	77.8294	593	2341	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	77.8185	581	2341	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	77.7314	588	2341	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	77.7226	597	2341	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	77.7023	505	2341	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	77.6967	481	2341	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	77.6176	617	2341	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	77.4221	450	2341	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	77.3683	430	2341	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	77.253	400	2341	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.3223	277	2341	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.2865	366	2341	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.0254	292	2341	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:10,847] [INFO] DFAST Taxonomy check result was written to GCF_014205765.1_ASM1420576v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:10,847] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:10,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:10,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f0cf6fb-0467-4906-ac35-51f3fcc5a41a/dqc_reference/checkm_data
[2024-01-24 14:31:10,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:10,920] [INFO] Task started: CheckM
[2024-01-24 14:31:10,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205765.1_ASM1420576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205765.1_ASM1420576v1_genomic.fna/checkm_input GCF_014205765.1_ASM1420576v1_genomic.fna/checkm_result
[2024-01-24 14:32:17,768] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:17,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:17,792] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:17,792] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:17,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205765.1_ASM1420576v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:17,793] [INFO] Task started: Blastn
[2024-01-24 14:32:17,794] [INFO] Running command: blastn -query GCF_014205765.1_ASM1420576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f0cf6fb-0467-4906-ac35-51f3fcc5a41a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205765.1_ASM1420576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:19,569] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:19,573] [INFO] Selected 6 target genomes.
[2024-01-24 14:32:19,574] [INFO] Target genome list was writen to GCF_014205765.1_ASM1420576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:19,579] [INFO] Task started: fastANI
[2024-01-24 14:32:19,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e7e0d8d-490f-429a-9d2a-c3176152fc80/GCF_014205765.1_ASM1420576v1_genomic.fna.gz --refList GCF_014205765.1_ASM1420576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205765.1_ASM1420576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:31,808] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:31,817] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:31,817] [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_014205765.1	s__Nitrospirillum iridis	100.0	2340	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000333275.1	s__Nitrospirillum sp000333275	87.8466	1555	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828045.1	s__Nitrospirillum amazonense_C	87.3827	1705	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730165.1	s__Nitrospirillum amazonense	87.2544	1747	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	97.38	95.62	0.93	0.89	4	-
GCF_007828035.1	s__Nitrospirillum amazonense_A	87.2327	1714	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827955.1	s__Nitrospirillum amazonense_B	86.9017	1670	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:31,819] [INFO] GTDB search result was written to GCF_014205765.1_ASM1420576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:31,819] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:31,823] [INFO] DFAST_QC result json was written to GCF_014205765.1_ASM1420576v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:31,823] [INFO] DFAST_QC completed!
[2024-01-24 14:32:31,823] [INFO] Total running time: 0h2m16s