[2023-06-28 15:07:13,215] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:07:13,217] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:07:13,217] [INFO] DQC Reference Directory: /var/lib/cwl/stgc44abe72-3660-4a2b-82f7-e3c8d5a9d96f/dqc_reference
[2023-06-28 15:07:14,367] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:07:14,368] [INFO] Task started: Prodigal
[2023-06-28 15:07:14,368] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ab668e1-a5ba-4ca0-88d9-253647486d63/GCA_020851285.1_ASM2085128v1_genomic.fna.gz | prodigal -d GCA_020851285.1_ASM2085128v1_genomic.fna/cds.fna -a GCA_020851285.1_ASM2085128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:07:27,958] [INFO] Task succeeded: Prodigal
[2023-06-28 15:07:27,958] [INFO] Task started: HMMsearch
[2023-06-28 15:07:27,958] [INFO] Running command: hmmsearch --tblout GCA_020851285.1_ASM2085128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc44abe72-3660-4a2b-82f7-e3c8d5a9d96f/dqc_reference/reference_markers.hmm GCA_020851285.1_ASM2085128v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:07:28,197] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:07:28,198] [INFO] Found 6/6 markers.
[2023-06-28 15:07:28,238] [INFO] Query marker FASTA was written to GCA_020851285.1_ASM2085128v1_genomic.fna/markers.fasta
[2023-06-28 15:07:28,239] [INFO] Task started: Blastn
[2023-06-28 15:07:28,239] [INFO] Running command: blastn -query GCA_020851285.1_ASM2085128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc44abe72-3660-4a2b-82f7-e3c8d5a9d96f/dqc_reference/reference_markers.fasta -out GCA_020851285.1_ASM2085128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:07:28,854] [INFO] Task succeeded: Blastn
[2023-06-28 15:07:28,857] [INFO] Selected 29 target genomes.
[2023-06-28 15:07:28,858] [INFO] Target genome list was writen to GCA_020851285.1_ASM2085128v1_genomic.fna/target_genomes.txt
[2023-06-28 15:07:28,860] [INFO] Task started: fastANI
[2023-06-28 15:07:28,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ab668e1-a5ba-4ca0-88d9-253647486d63/GCA_020851285.1_ASM2085128v1_genomic.fna.gz --refList GCA_020851285.1_ASM2085128v1_genomic.fna/target_genomes.txt --output GCA_020851285.1_ASM2085128v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:07:48,684] [INFO] Task succeeded: fastANI
[2023-06-28 15:07:48,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc44abe72-3660-4a2b-82f7-e3c8d5a9d96f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:07:48,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc44abe72-3660-4a2b-82f7-e3c8d5a9d96f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:07:48,699] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:07:48,699] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 15:07:48,699] [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
Corallococcus exercitus	strain=AB043A	GCA_003611585.1	2316736	2316736	type	True	74.9603	77	1683	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	74.9249	57	1683	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	74.9215	58	1683	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.9016	97	1683	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.899	103	1683	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	74.8372	52	1683	95	below_threshold
Saccharomonospora saliphila	strain=YIM 90502	GCA_000383795.1	369829	369829	type	True	74.829	51	1683	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	74.8289	65	1683	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	74.7691	73	1683	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	74.7638	72	1683	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	74.7477	52	1683	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	74.7439	59	1683	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	74.7279	84	1683	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	74.7082	62	1683	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	74.7082	62	1683	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	74.7082	62	1683	95	below_threshold
Kineococcus xinjiangensis	strain=DSM 22857	GCA_002934625.1	512762	512762	type	True	74.6909	66	1683	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	74.6672	85	1683	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:07:48,701] [INFO] DFAST Taxonomy check result was written to GCA_020851285.1_ASM2085128v1_genomic.fna/tc_result.tsv
[2023-06-28 15:07:48,701] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:07:48,702] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:07:48,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc44abe72-3660-4a2b-82f7-e3c8d5a9d96f/dqc_reference/checkm_data
[2023-06-28 15:07:48,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:07:48,751] [INFO] Task started: CheckM
[2023-06-28 15:07:48,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020851285.1_ASM2085128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020851285.1_ASM2085128v1_genomic.fna/checkm_input GCA_020851285.1_ASM2085128v1_genomic.fna/checkm_result
[2023-06-28 15:08:31,283] [INFO] Task succeeded: CheckM
[2023-06-28 15:08:31,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:08:31,302] [INFO] ===== Completeness check finished =====
[2023-06-28 15:08:31,303] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:08:31,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020851285.1_ASM2085128v1_genomic.fna/markers.fasta)
[2023-06-28 15:08:31,303] [INFO] Task started: Blastn
[2023-06-28 15:08:31,303] [INFO] Running command: blastn -query GCA_020851285.1_ASM2085128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc44abe72-3660-4a2b-82f7-e3c8d5a9d96f/dqc_reference/reference_markers_gtdb.fasta -out GCA_020851285.1_ASM2085128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:08:32,148] [INFO] Task succeeded: Blastn
[2023-06-28 15:08:32,152] [INFO] Selected 26 target genomes.
[2023-06-28 15:08:32,152] [INFO] Target genome list was writen to GCA_020851285.1_ASM2085128v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:08:32,186] [INFO] Task started: fastANI
[2023-06-28 15:08:32,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ab668e1-a5ba-4ca0-88d9-253647486d63/GCA_020851285.1_ASM2085128v1_genomic.fna.gz --refList GCA_020851285.1_ASM2085128v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020851285.1_ASM2085128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:08:48,839] [INFO] Task succeeded: fastANI
[2023-06-28 15:08:48,853] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 15:08:48,853] [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_016712505.1	s__JADJQY01 sp016712505	99.0871	1563	1683	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__CAIMUX01;f__CAIMUX01;g__JADJQY01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016867495.1	s__VGJL01 sp016867495	76.1845	64	1683	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__CAIMUX01;f__VGJL01;g__VGJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014729815.1	s__WJJG01 sp014729815	75.7602	68	1683	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__CAIMUX01;f__WJJG01;g__WJJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867695.1	s__VGIY01 sp016867695	75.6596	88	1683	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__CAIMUX01;f__WJJG01;g__VGIY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298115.1	s__RBG-13-68-16 sp004298115	75.2456	78	1683	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__RBG-13-68-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011357805.1	s__DSQF01 sp011357805	75.1941	105	1683	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__RBG-16-71-46;f__RBG-16-71-46;g__DSQF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215625.1	s__CAIXRL01 sp016215625	75.1315	96	1683	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__RBG-16-71-46;f__RBG-16-71-46;g__CAIXRL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489145.1	s__S143-5 sp015489145	75.1241	77	1683	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__S143-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	74.9754	63	1683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	74.9016	97	1683	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383795.1	s__Saccharomonospora saliphila	74.829	51	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001788415.1	s__UBA12499 sp001788415	74.7981	60	1683	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__UBA12499	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016188005.1	s__UBA12499 sp016188005	74.7724	62	1683	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__UBA12499	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	74.7638	72	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795105.1	s__Streptomyces sp004795105	74.7264	90	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509485.1	s__Streptomyces sp001509485	74.7093	105	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934625.1	s__Kineococcus xinjiangensis	74.6894	65	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522095.1	s__Nocardioides sp004522095	74.6026	65	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:08:48,868] [INFO] GTDB search result was written to GCA_020851285.1_ASM2085128v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:08:48,869] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:08:48,873] [INFO] DFAST_QC result json was written to GCA_020851285.1_ASM2085128v1_genomic.fna/dqc_result.json
[2023-06-28 15:08:48,873] [INFO] DFAST_QC completed!
[2023-06-28 15:08:48,874] [INFO] Total running time: 0h1m36s