[2024-01-24 11:26:12,645] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg949f7919-c765-4031-916c-1fc02cb89b50/dqc_reference
[2024-01-24 11:26:14,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,131] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,132] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc7e76a3-7872-4efc-8c46-c5237921b139/GCF_002019695.1_ASM201969v1_genomic.fna.gz | prodigal -d GCF_002019695.1_ASM201969v1_genomic.fna/cds.fna -a GCF_002019695.1_ASM201969v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:26,138] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:26,138] [INFO] Task started: HMMsearch
[2024-01-24 11:26:26,138] [INFO] Running command: hmmsearch --tblout GCF_002019695.1_ASM201969v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg949f7919-c765-4031-916c-1fc02cb89b50/dqc_reference/reference_markers.hmm GCF_002019695.1_ASM201969v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:26,482] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:26,484] [INFO] Found 6/6 markers.
[2024-01-24 11:26:26,547] [INFO] Query marker FASTA was written to GCF_002019695.1_ASM201969v1_genomic.fna/markers.fasta
[2024-01-24 11:26:26,548] [INFO] Task started: Blastn
[2024-01-24 11:26:26,548] [INFO] Running command: blastn -query GCF_002019695.1_ASM201969v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg949f7919-c765-4031-916c-1fc02cb89b50/dqc_reference/reference_markers.fasta -out GCF_002019695.1_ASM201969v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:27,191] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:27,195] [INFO] Selected 31 target genomes.
[2024-01-24 11:26:27,195] [INFO] Target genome list was writen to GCF_002019695.1_ASM201969v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:27,221] [INFO] Task started: fastANI
[2024-01-24 11:26:27,221] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc7e76a3-7872-4efc-8c46-c5237921b139/GCF_002019695.1_ASM201969v1_genomic.fna.gz --refList GCF_002019695.1_ASM201969v1_genomic.fna/target_genomes.txt --output GCF_002019695.1_ASM201969v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:51,681] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:51,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg949f7919-c765-4031-916c-1fc02cb89b50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:51,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg949f7919-c765-4031-916c-1fc02cb89b50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:51,693] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:51,693] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:51,693] [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
Evansella clarkii	strain=DSM 8720	GCA_002019695.1	79879	79879	type	True	99.9992	1816	1822	95	conclusive
Priestia abyssalis	strain=DSM 25875	GCA_002019595.1	1221450	1221450	type	True	79.7265	50	1822	95	below_threshold
Salipaludibacillus agaradhaerens	strain=DSM 8721	GCA_002019735.1	76935	76935	type	True	79.3085	93	1822	95	below_threshold
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	79.0425	136	1822	95	below_threshold
Evansella cellulosilytica	strain=DSM 2522	GCA_000177235.2	1413	1413	type	True	78.9761	138	1822	95	below_threshold
Alteribacter populi	strain=FJAT-45347	GCA_002352765.2	2011011	2011011	type	True	78.0586	102	1822	95	below_threshold
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	77.7291	52	1822	95	below_threshold
Evansella tamaricis	strain=CGMCC 1.15917	GCA_019042215.1	2069301	2069301	type	True	77.4944	122	1822	95	below_threshold
Salipaludibacillus aurantiacus	strain=S9	GCA_900111295.1	1601833	1601833	type	True	77.2089	125	1822	95	below_threshold
Alteribacter salitolerans	strain=APA H-16(1)	GCA_016901055.1	2912333	2912333	type	True	77.2024	109	1822	95	below_threshold
Alteribacter natronophilus	strain=M30	GCA_006007885.1	2583810	2583810	type	True	76.9632	86	1822	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	75.9216	56	1822	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:51,695] [INFO] DFAST Taxonomy check result was written to GCF_002019695.1_ASM201969v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:51,695] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:51,696] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:51,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg949f7919-c765-4031-916c-1fc02cb89b50/dqc_reference/checkm_data
[2024-01-24 11:26:51,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:51,749] [INFO] Task started: CheckM
[2024-01-24 11:26:51,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002019695.1_ASM201969v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002019695.1_ASM201969v1_genomic.fna/checkm_input GCF_002019695.1_ASM201969v1_genomic.fna/checkm_result
[2024-01-24 11:27:31,083] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:31,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:31,105] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:31,106] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:31,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002019695.1_ASM201969v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:31,106] [INFO] Task started: Blastn
[2024-01-24 11:27:31,106] [INFO] Running command: blastn -query GCF_002019695.1_ASM201969v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg949f7919-c765-4031-916c-1fc02cb89b50/dqc_reference/reference_markers_gtdb.fasta -out GCF_002019695.1_ASM201969v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:31,878] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:31,882] [INFO] Selected 30 target genomes.
[2024-01-24 11:27:31,883] [INFO] Target genome list was writen to GCF_002019695.1_ASM201969v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:31,913] [INFO] Task started: fastANI
[2024-01-24 11:27:31,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc7e76a3-7872-4efc-8c46-c5237921b139/GCF_002019695.1_ASM201969v1_genomic.fna.gz --refList GCF_002019695.1_ASM201969v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002019695.1_ASM201969v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:55,293] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:55,306] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:55,306] [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_002019695.1	s__Evansella clarkii	99.9992	1817	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	98.30	98.30	0.93	0.93	2	conclusive
GCF_002563635.1	s__Anaerobacillus_A sp002563635	80.2857	53	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	96.09	95.80	0.90	0.90	3	-
GCF_900199725.1	s__Cytobacillus massiliigabonensis	79.6034	63	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002335745.1	s__FJAT-44876 sp002335745	79.2966	174	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__FJAT-44876	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019735.1	s__Salipaludibacillus agaradhaerens	79.1329	92	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000177235.2	s__Evansella cellulosilytica	79.0567	138	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002352765.1	s__Alteribacter populi	78.0249	101	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	99.66	99.66	0.95	0.95	2	-
GCF_000621445.1	s__Bacillus_AO bogoriensis	77.7532	53	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019042215.1	s__Evansella tamaricis	77.4902	123	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107275.1	s__Evansella caseinilytica	77.4801	98	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710255.1	s__Alteribacter sp003710255	77.3827	100	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	98.04	98.04	0.95	0.95	2	-
GCF_900111295.1	s__Salipaludibacillus aurantiacus	77.2089	125	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006007885.1	s__Alteribacter natronophilus	76.9955	86	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732485.2	s__Metabacillus_B sp000732485	76.5645	51	1822	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:55,308] [INFO] GTDB search result was written to GCF_002019695.1_ASM201969v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:55,309] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:55,312] [INFO] DFAST_QC result json was written to GCF_002019695.1_ASM201969v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:55,313] [INFO] DFAST_QC completed!
[2024-01-24 11:27:55,313] [INFO] Total running time: 0h1m43s