[2024-01-24 12:22:48,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg9cf3a8ca-102b-4247-aecb-e79a7370406a/dqc_reference
[2024-01-24 12:22:49,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,880] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,880] [INFO] Running command: gunzip -c /var/lib/cwl/stg92ad21a1-6e81-4b7e-851f-5afbc79f30c0/GCF_000285535.1_ASM28553v1_genomic.fna.gz | prodigal -d GCF_000285535.1_ASM28553v1_genomic.fna/cds.fna -a GCF_000285535.1_ASM28553v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:59,920] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:59,920] [INFO] Task started: HMMsearch
[2024-01-24 12:22:59,920] [INFO] Running command: hmmsearch --tblout GCF_000285535.1_ASM28553v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9cf3a8ca-102b-4247-aecb-e79a7370406a/dqc_reference/reference_markers.hmm GCF_000285535.1_ASM28553v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:00,238] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:00,240] [INFO] Found 6/6 markers.
[2024-01-24 12:23:00,301] [INFO] Query marker FASTA was written to GCF_000285535.1_ASM28553v1_genomic.fna/markers.fasta
[2024-01-24 12:23:00,301] [INFO] Task started: Blastn
[2024-01-24 12:23:00,302] [INFO] Running command: blastn -query GCF_000285535.1_ASM28553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cf3a8ca-102b-4247-aecb-e79a7370406a/dqc_reference/reference_markers.fasta -out GCF_000285535.1_ASM28553v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:00,959] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:00,967] [INFO] Selected 29 target genomes.
[2024-01-24 12:23:00,968] [INFO] Target genome list was writen to GCF_000285535.1_ASM28553v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:00,982] [INFO] Task started: fastANI
[2024-01-24 12:23:00,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg92ad21a1-6e81-4b7e-851f-5afbc79f30c0/GCF_000285535.1_ASM28553v1_genomic.fna.gz --refList GCF_000285535.1_ASM28553v1_genomic.fna/target_genomes.txt --output GCF_000285535.1_ASM28553v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:22,568] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:22,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9cf3a8ca-102b-4247-aecb-e79a7370406a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:22,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9cf3a8ca-102b-4247-aecb-e79a7370406a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:22,595] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:22,596] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:22,596] [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
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	83.0787	1041	1538	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	77.6454	177	1538	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	77.3712	169	1538	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	77.3016	138	1538	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	77.2538	138	1538	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_003055085.1	46224	46224	type	True	77.092	99	1538	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	77.073	59	1538	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	76.9774	106	1538	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	76.9089	69	1538	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	76.8809	155	1538	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	76.8662	109	1538	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	76.8073	160	1538	95	below_threshold
Jeotgalibacillus alimentarius	strain=YKJ-13	GCA_000829445.1	135826	135826	type	True	76.7842	51	1538	95	below_threshold
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	76.755	122	1538	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	76.7538	64	1538	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.6952	112	1538	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.693	90	1538	95	below_threshold
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	76.6886	74	1538	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.6619	98	1538	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.6052	112	1538	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.5989	119	1538	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	76.4166	77	1538	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.3539	122	1538	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	76.3381	123	1538	95	below_threshold
Virgibacillus halotolerans	strain=DSM 25060	GCA_016908515.1	1071053	1071053	type	True	76.1161	51	1538	95	below_threshold
Bacillus solimangrovi	strain=GH2-4	GCA_001742425.1	1305675	1305675	type	True	76.0172	78	1538	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:22,598] [INFO] DFAST Taxonomy check result was written to GCF_000285535.1_ASM28553v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:22,599] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:22,599] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:22,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9cf3a8ca-102b-4247-aecb-e79a7370406a/dqc_reference/checkm_data
[2024-01-24 12:23:22,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:22,645] [INFO] Task started: CheckM
[2024-01-24 12:23:22,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000285535.1_ASM28553v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000285535.1_ASM28553v1_genomic.fna/checkm_input GCF_000285535.1_ASM28553v1_genomic.fna/checkm_result
[2024-01-24 12:23:56,902] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:56,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:56,923] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:56,923] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:56,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000285535.1_ASM28553v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:56,924] [INFO] Task started: Blastn
[2024-01-24 12:23:56,924] [INFO] Running command: blastn -query GCF_000285535.1_ASM28553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cf3a8ca-102b-4247-aecb-e79a7370406a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000285535.1_ASM28553v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:57,716] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:57,721] [INFO] Selected 7 target genomes.
[2024-01-24 12:23:57,721] [INFO] Target genome list was writen to GCF_000285535.1_ASM28553v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:57,727] [INFO] Task started: fastANI
[2024-01-24 12:23:57,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg92ad21a1-6e81-4b7e-851f-5afbc79f30c0/GCF_000285535.1_ASM28553v1_genomic.fna.gz --refList GCF_000285535.1_ASM28553v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000285535.1_ASM28553v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:05,965] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:05,976] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:05,976] [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_000285535.1	s__Fredinandcohnia timonensis	99.9999	1532	1538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003400205.1	s__Fredinandcohnia sp003400205	83.0933	1021	1538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734215.1	s__Fredinandcohnia onubensis	83.0727	1042	1538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799755.1	s__Fredinandcohnia timonensis_A	82.9652	988	1538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734285.1	s__Fredinandcohnia onubensis_A	82.8699	1027	1538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439915.1	s__Fredinandcohnia humi	82.7679	970	1538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156865.1	s__Fredinandcohnia sinesaloumensis	81.2542	828	1538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:05,978] [INFO] GTDB search result was written to GCF_000285535.1_ASM28553v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:05,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:05,983] [INFO] DFAST_QC result json was written to GCF_000285535.1_ASM28553v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:05,983] [INFO] DFAST_QC completed!
[2024-01-24 12:24:05,983] [INFO] Total running time: 0h1m17s