[2024-01-24 12:37:25,071] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:25,074] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:25,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d532d53-86a3-4e50-964d-a27226b2b275/dqc_reference
[2024-01-24 12:37:26,356] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,357] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,357] [INFO] Running command: gunzip -c /var/lib/cwl/stg41756254-9078-4bcd-aeff-f73d96dcc451/GCF_019042215.1_ASM1904221v1_genomic.fna.gz | prodigal -d GCF_019042215.1_ASM1904221v1_genomic.fna/cds.fna -a GCF_019042215.1_ASM1904221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:36,502] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:36,503] [INFO] Task started: HMMsearch
[2024-01-24 12:37:36,503] [INFO] Running command: hmmsearch --tblout GCF_019042215.1_ASM1904221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d532d53-86a3-4e50-964d-a27226b2b275/dqc_reference/reference_markers.hmm GCF_019042215.1_ASM1904221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:36,833] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:36,836] [INFO] Found 6/6 markers.
[2024-01-24 12:37:36,876] [INFO] Query marker FASTA was written to GCF_019042215.1_ASM1904221v1_genomic.fna/markers.fasta
[2024-01-24 12:37:36,877] [INFO] Task started: Blastn
[2024-01-24 12:37:36,877] [INFO] Running command: blastn -query GCF_019042215.1_ASM1904221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d532d53-86a3-4e50-964d-a27226b2b275/dqc_reference/reference_markers.fasta -out GCF_019042215.1_ASM1904221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:37,475] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:37,478] [INFO] Selected 26 target genomes.
[2024-01-24 12:37:37,479] [INFO] Target genome list was writen to GCF_019042215.1_ASM1904221v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:37,512] [INFO] Task started: fastANI
[2024-01-24 12:37:37,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg41756254-9078-4bcd-aeff-f73d96dcc451/GCF_019042215.1_ASM1904221v1_genomic.fna.gz --refList GCF_019042215.1_ASM1904221v1_genomic.fna/target_genomes.txt --output GCF_019042215.1_ASM1904221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:54,900] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:54,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d532d53-86a3-4e50-964d-a27226b2b275/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:54,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d532d53-86a3-4e50-964d-a27226b2b275/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:54,911] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:54,912] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:54,912] [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 tamaricis	strain=CGMCC 1.15917	GCA_019042215.1	2069301	2069301	type	True	100.0	1623	1640	95	conclusive
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	77.5713	71	1640	95	below_threshold
Bacillus alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	77.1553	81	1640	95	below_threshold
Alteribacter aurantiacus	strain=DSM 18675	GCA_000429705.1	254410	254410	type	True	77.0514	66	1640	95	below_threshold
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	76.9426	163	1640	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	76.7865	67	1640	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	76.6691	64	1640	95	below_threshold
Texcoconibacillus texcoconensis	strain=DSM 24696	GCA_014202575.1	1095777	1095777	type	True	76.6107	64	1640	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	76.1802	67	1640	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	76.0729	57	1640	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:54,914] [INFO] DFAST Taxonomy check result was written to GCF_019042215.1_ASM1904221v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:54,914] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:54,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:54,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d532d53-86a3-4e50-964d-a27226b2b275/dqc_reference/checkm_data
[2024-01-24 12:37:54,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:54,970] [INFO] Task started: CheckM
[2024-01-24 12:37:54,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019042215.1_ASM1904221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019042215.1_ASM1904221v1_genomic.fna/checkm_input GCF_019042215.1_ASM1904221v1_genomic.fna/checkm_result
[2024-01-24 12:38:29,865] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:29,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:29,886] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:29,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:29,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019042215.1_ASM1904221v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:29,888] [INFO] Task started: Blastn
[2024-01-24 12:38:29,888] [INFO] Running command: blastn -query GCF_019042215.1_ASM1904221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d532d53-86a3-4e50-964d-a27226b2b275/dqc_reference/reference_markers_gtdb.fasta -out GCF_019042215.1_ASM1904221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:30,616] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:30,620] [INFO] Selected 25 target genomes.
[2024-01-24 12:38:30,620] [INFO] Target genome list was writen to GCF_019042215.1_ASM1904221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:30,639] [INFO] Task started: fastANI
[2024-01-24 12:38:30,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg41756254-9078-4bcd-aeff-f73d96dcc451/GCF_019042215.1_ASM1904221v1_genomic.fna.gz --refList GCF_019042215.1_ASM1904221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019042215.1_ASM1904221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:48,317] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:48,332] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:48,332] [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_019042215.1	s__Evansella tamaricis	100.0	1623	1640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000621445.1	s__Bacillus_AO bogoriensis	77.5135	71	1640	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_002019795.1	s__Bacillus_AO alkalicellulosilyticus	77.1608	81	1640	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_000429705.1	s__Alteribacter aurantiacus	77.0618	65	1640	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_002335805.1	s__FJAT-45350 sp002335805	76.9348	58	1640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__FJAT-45350	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787375.1	s__Bacillus_L okhensis	76.8225	66	1640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797395.1	s__45385 sp002797395	76.7327	60	1640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202575.1	s__Texcoconibacillus texcoconensis	76.6414	63	1640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Texcoconibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	76.6398	63	1640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
GCF_017939705.1	s__Bacillus_L sp017939705	76.0282	66	1640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:48,334] [INFO] GTDB search result was written to GCF_019042215.1_ASM1904221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:48,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:48,337] [INFO] DFAST_QC result json was written to GCF_019042215.1_ASM1904221v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:48,337] [INFO] DFAST_QC completed!
[2024-01-24 12:38:48,337] [INFO] Total running time: 0h1m23s