[2023-06-19 07:50:08,882] [INFO] DFAST_QC pipeline started.
[2023-06-19 07:50:08,885] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 07:50:08,886] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6fa022f-b049-41ff-b60a-6a8ee7e45070/dqc_reference
[2023-06-19 07:50:10,180] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 07:50:10,181] [INFO] Task started: Prodigal
[2023-06-19 07:50:10,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a9f8c2b-90af-44f1-b9f3-3068826b81e3/GCA_018676175.1_ASM1867617v1_genomic.fna.gz | prodigal -d GCA_018676175.1_ASM1867617v1_genomic.fna/cds.fna -a GCA_018676175.1_ASM1867617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 07:50:19,125] [INFO] Task succeeded: Prodigal
[2023-06-19 07:50:19,126] [INFO] Task started: HMMsearch
[2023-06-19 07:50:19,126] [INFO] Running command: hmmsearch --tblout GCA_018676175.1_ASM1867617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6fa022f-b049-41ff-b60a-6a8ee7e45070/dqc_reference/reference_markers.hmm GCA_018676175.1_ASM1867617v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 07:50:19,396] [INFO] Task succeeded: HMMsearch
[2023-06-19 07:50:19,398] [INFO] Found 6/6 markers.
[2023-06-19 07:50:19,439] [INFO] Query marker FASTA was written to GCA_018676175.1_ASM1867617v1_genomic.fna/markers.fasta
[2023-06-19 07:50:19,439] [INFO] Task started: Blastn
[2023-06-19 07:50:19,440] [INFO] Running command: blastn -query GCA_018676175.1_ASM1867617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6fa022f-b049-41ff-b60a-6a8ee7e45070/dqc_reference/reference_markers.fasta -out GCA_018676175.1_ASM1867617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:50:20,137] [INFO] Task succeeded: Blastn
[2023-06-19 07:50:20,141] [INFO] Selected 27 target genomes.
[2023-06-19 07:50:20,141] [INFO] Target genome list was writen to GCA_018676175.1_ASM1867617v1_genomic.fna/target_genomes.txt
[2023-06-19 07:50:20,146] [INFO] Task started: fastANI
[2023-06-19 07:50:20,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a9f8c2b-90af-44f1-b9f3-3068826b81e3/GCA_018676175.1_ASM1867617v1_genomic.fna.gz --refList GCA_018676175.1_ASM1867617v1_genomic.fna/target_genomes.txt --output GCA_018676175.1_ASM1867617v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 07:50:38,303] [INFO] Task succeeded: fastANI
[2023-06-19 07:50:38,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6fa022f-b049-41ff-b60a-6a8ee7e45070/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 07:50:38,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6fa022f-b049-41ff-b60a-6a8ee7e45070/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 07:50:38,312] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 07:50:38,312] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 07:50:38,312] [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
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	75.804	60	818	95	below_threshold
Pelagibius litoralis	strain=DSM 21314	GCA_011683915.1	374515	374515	type	True	75.7404	61	818	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.634	90	818	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	75.5949	63	818	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.3357	64	818	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	75.2898	61	818	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	75.2787	65	818	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	75.2706	50	818	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	75.2479	61	818	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 07:50:38,314] [INFO] DFAST Taxonomy check result was written to GCA_018676175.1_ASM1867617v1_genomic.fna/tc_result.tsv
[2023-06-19 07:50:38,315] [INFO] ===== Taxonomy check completed =====
[2023-06-19 07:50:38,315] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 07:50:38,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6fa022f-b049-41ff-b60a-6a8ee7e45070/dqc_reference/checkm_data
[2023-06-19 07:50:38,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 07:50:38,357] [INFO] Task started: CheckM
[2023-06-19 07:50:38,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018676175.1_ASM1867617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018676175.1_ASM1867617v1_genomic.fna/checkm_input GCA_018676175.1_ASM1867617v1_genomic.fna/checkm_result
[2023-06-19 07:51:09,620] [INFO] Task succeeded: CheckM
[2023-06-19 07:51:09,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.74%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 07:51:09,645] [INFO] ===== Completeness check finished =====
[2023-06-19 07:51:09,646] [INFO] ===== Start GTDB Search =====
[2023-06-19 07:51:09,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018676175.1_ASM1867617v1_genomic.fna/markers.fasta)
[2023-06-19 07:51:09,647] [INFO] Task started: Blastn
[2023-06-19 07:51:09,647] [INFO] Running command: blastn -query GCA_018676175.1_ASM1867617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6fa022f-b049-41ff-b60a-6a8ee7e45070/dqc_reference/reference_markers_gtdb.fasta -out GCA_018676175.1_ASM1867617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:51:10,778] [INFO] Task succeeded: Blastn
[2023-06-19 07:51:10,783] [INFO] Selected 28 target genomes.
[2023-06-19 07:51:10,784] [INFO] Target genome list was writen to GCA_018676175.1_ASM1867617v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 07:51:10,796] [INFO] Task started: fastANI
[2023-06-19 07:51:10,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a9f8c2b-90af-44f1-b9f3-3068826b81e3/GCA_018676175.1_ASM1867617v1_genomic.fna.gz --refList GCA_018676175.1_ASM1867617v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018676175.1_ASM1867617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 07:51:31,729] [INFO] Task succeeded: fastANI
[2023-06-19 07:51:31,741] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 07:51:31,742] [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
GCA_018700655.1	s__SP197 sp018700655	99.2587	699	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	99.23	99.15	0.84	0.82	5	conclusive
GCA_002722885.1	s__SP197 sp002722885	78.9082	396	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014323865.1	s__SP197 sp014323865	78.1571	247	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363235.1	s__Dongia mobilis	75.804	60	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116095.1	s__Azospirillum sp003116095	75.5648	70	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	75.5372	81	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903915535.1	s__Reyranella aerosaccus_C	75.4662	57	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.05	99.05	0.90	0.90	2	-
GCF_008365375.1	s__Azospirillum sp008365375	75.3795	66	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283655.1	s__Azospirillum lipoferum_C	75.3491	59	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639105.2	s__Azospirillum humicireducens	75.2787	65	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 07:51:31,744] [INFO] GTDB search result was written to GCA_018676175.1_ASM1867617v1_genomic.fna/result_gtdb.tsv
[2023-06-19 07:51:31,744] [INFO] ===== GTDB Search completed =====
[2023-06-19 07:51:31,748] [INFO] DFAST_QC result json was written to GCA_018676175.1_ASM1867617v1_genomic.fna/dqc_result.json
[2023-06-19 07:51:31,748] [INFO] DFAST_QC completed!
[2023-06-19 07:51:31,748] [INFO] Total running time: 0h1m23s