[2024-01-24 13:28:15,352] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:15,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:15,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a9739b1-a3c5-4555-96f9-d307023fa4ed/dqc_reference
[2024-01-24 13:28:16,589] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:16,589] [INFO] Task started: Prodigal
[2024-01-24 13:28:16,590] [INFO] Running command: gunzip -c /var/lib/cwl/stg49a72edb-6de2-4faa-b133-93b946829d62/GCF_014596085.1_ASM1459608v1_genomic.fna.gz | prodigal -d GCF_014596085.1_ASM1459608v1_genomic.fna/cds.fna -a GCF_014596085.1_ASM1459608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:35,585] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:35,586] [INFO] Task started: HMMsearch
[2024-01-24 13:28:35,586] [INFO] Running command: hmmsearch --tblout GCF_014596085.1_ASM1459608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a9739b1-a3c5-4555-96f9-d307023fa4ed/dqc_reference/reference_markers.hmm GCF_014596085.1_ASM1459608v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:35,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:35,952] [INFO] Found 6/6 markers.
[2024-01-24 13:28:36,020] [INFO] Query marker FASTA was written to GCF_014596085.1_ASM1459608v1_genomic.fna/markers.fasta
[2024-01-24 13:28:36,020] [INFO] Task started: Blastn
[2024-01-24 13:28:36,020] [INFO] Running command: blastn -query GCF_014596085.1_ASM1459608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a9739b1-a3c5-4555-96f9-d307023fa4ed/dqc_reference/reference_markers.fasta -out GCF_014596085.1_ASM1459608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:37,156] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:37,159] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:37,159] [INFO] Target genome list was writen to GCF_014596085.1_ASM1459608v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:37,172] [INFO] Task started: fastANI
[2024-01-24 13:28:37,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg49a72edb-6de2-4faa-b133-93b946829d62/GCF_014596085.1_ASM1459608v1_genomic.fna.gz --refList GCF_014596085.1_ASM1459608v1_genomic.fna/target_genomes.txt --output GCF_014596085.1_ASM1459608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:58,060] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:58,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a9739b1-a3c5-4555-96f9-d307023fa4ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:58,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a9739b1-a3c5-4555-96f9-d307023fa4ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:58,071] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:58,071] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:58,071] [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 tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	100.0	2062	2066	95	conclusive
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	94.454	1844	2066	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	94.4392	1838	2066	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	94.3775	1847	2066	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	94.046	1796	2066	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	94.0307	1725	2066	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	94.0278	1504	2066	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	94.0105	1804	2066	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	93.9672	1790	2066	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	81.173	941	2066	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	78.3826	653	2066	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.9453	247	2066	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:58,073] [INFO] DFAST Taxonomy check result was written to GCF_014596085.1_ASM1459608v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:58,074] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:58,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:58,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a9739b1-a3c5-4555-96f9-d307023fa4ed/dqc_reference/checkm_data
[2024-01-24 13:28:58,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:58,133] [INFO] Task started: CheckM
[2024-01-24 13:28:58,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014596085.1_ASM1459608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014596085.1_ASM1459608v1_genomic.fna/checkm_input GCF_014596085.1_ASM1459608v1_genomic.fna/checkm_result
[2024-01-24 13:29:52,698] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:52,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:52,722] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:52,722] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:52,723] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014596085.1_ASM1459608v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:52,723] [INFO] Task started: Blastn
[2024-01-24 13:29:52,723] [INFO] Running command: blastn -query GCF_014596085.1_ASM1459608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a9739b1-a3c5-4555-96f9-d307023fa4ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_014596085.1_ASM1459608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:54,904] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:54,908] [INFO] Selected 9 target genomes.
[2024-01-24 13:29:54,908] [INFO] Target genome list was writen to GCF_014596085.1_ASM1459608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:54,917] [INFO] Task started: fastANI
[2024-01-24 13:29:54,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg49a72edb-6de2-4faa-b133-93b946829d62/GCF_014596085.1_ASM1459608v1_genomic.fna.gz --refList GCF_014596085.1_ASM1459608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014596085.1_ASM1459608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:12,655] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:12,663] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:12,663] [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_002245955.1	s__Azospirillum brasilense_A	97.4596	1877	2066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.48	97.48	0.91	0.91	2	conclusive
GCF_003119115.1	s__Azospirillum sp003119115	94.4541	1866	2066	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	94.4302	1839	2066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	97.20	95.48	0.90	0.83	11	-
GCF_008365405.1	s__Azospirillum brasilense_D	94.3542	1778	2066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827795.1	s__Azospirillum brasilense_E	94.2561	1746	2066	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	94.1736	1825	2066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	94.0996	1714	2066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_007827815.1	s__Azospirillum brasilense_C	94.0675	1843	2066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCF_001315015.1	s__Azospirillum brasilense	94.057	1795	2066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:12,665] [INFO] GTDB search result was written to GCF_014596085.1_ASM1459608v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:12,665] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:12,668] [INFO] DFAST_QC result json was written to GCF_014596085.1_ASM1459608v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:12,669] [INFO] DFAST_QC completed!
[2024-01-24 13:30:12,669] [INFO] Total running time: 0h1m57s