[2024-01-24 14:39:45,835] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,838] [INFO] DQC Reference Directory: /var/lib/cwl/stga888bfa6-8662-49f0-8e10-79730d773a9f/dqc_reference
[2024-01-24 14:39:48,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:48,366] [INFO] Task started: Prodigal
[2024-01-24 14:39:48,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cc71b4f-5a43-4905-b471-94aef15e0e05/GCF_014202575.1_ASM1420257v1_genomic.fna.gz | prodigal -d GCF_014202575.1_ASM1420257v1_genomic.fna/cds.fna -a GCF_014202575.1_ASM1420257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:56,086] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:56,086] [INFO] Task started: HMMsearch
[2024-01-24 14:39:56,086] [INFO] Running command: hmmsearch --tblout GCF_014202575.1_ASM1420257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga888bfa6-8662-49f0-8e10-79730d773a9f/dqc_reference/reference_markers.hmm GCF_014202575.1_ASM1420257v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:56,390] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:56,391] [INFO] Found 6/6 markers.
[2024-01-24 14:39:56,424] [INFO] Query marker FASTA was written to GCF_014202575.1_ASM1420257v1_genomic.fna/markers.fasta
[2024-01-24 14:39:56,424] [INFO] Task started: Blastn
[2024-01-24 14:39:56,424] [INFO] Running command: blastn -query GCF_014202575.1_ASM1420257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga888bfa6-8662-49f0-8e10-79730d773a9f/dqc_reference/reference_markers.fasta -out GCF_014202575.1_ASM1420257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:57,066] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:57,071] [INFO] Selected 26 target genomes.
[2024-01-24 14:39:57,071] [INFO] Target genome list was writen to GCF_014202575.1_ASM1420257v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:57,087] [INFO] Task started: fastANI
[2024-01-24 14:39:57,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cc71b4f-5a43-4905-b471-94aef15e0e05/GCF_014202575.1_ASM1420257v1_genomic.fna.gz --refList GCF_014202575.1_ASM1420257v1_genomic.fna/target_genomes.txt --output GCF_014202575.1_ASM1420257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:15,713] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:15,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga888bfa6-8662-49f0-8e10-79730d773a9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:15,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga888bfa6-8662-49f0-8e10-79730d773a9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:15,723] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:15,723] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:15,723] [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
Texcoconibacillus texcoconensis	strain=DSM 24696	GCA_014202575.1	1095777	1095777	type	True	100.0	1117	1119	95	conclusive
Salipaludibacillus keqinensis	strain=KQ-12	GCA_003226325.1	2045207	2045207	type	True	77.1761	52	1119	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	77.1061	71	1119	95	below_threshold
Anaerobacillus alkalidiazotrophicus	strain=DSM 22531	GCA_001866055.1	472963	472963	type	True	76.9337	54	1119	95	below_threshold
Salipaludibacillus aurantiacus	strain=S9	GCA_900111295.1	1601833	1601833	type	True	76.8039	53	1119	95	below_threshold
Evansella tamaricis	strain=CGMCC 1.15917	GCA_019042215.1	2069301	2069301	type	True	76.6484	65	1119	95	below_threshold
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	76.5539	55	1119	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	76.4951	54	1119	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.2992	52	1119	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	76.1802	63	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:15,726] [INFO] DFAST Taxonomy check result was written to GCF_014202575.1_ASM1420257v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:15,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:15,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:15,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga888bfa6-8662-49f0-8e10-79730d773a9f/dqc_reference/checkm_data
[2024-01-24 14:40:15,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:15,768] [INFO] Task started: CheckM
[2024-01-24 14:40:15,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202575.1_ASM1420257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202575.1_ASM1420257v1_genomic.fna/checkm_input GCF_014202575.1_ASM1420257v1_genomic.fna/checkm_result
[2024-01-24 14:40:45,717] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:45,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:45,742] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:45,742] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:45,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202575.1_ASM1420257v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:45,744] [INFO] Task started: Blastn
[2024-01-24 14:40:45,744] [INFO] Running command: blastn -query GCF_014202575.1_ASM1420257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga888bfa6-8662-49f0-8e10-79730d773a9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202575.1_ASM1420257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:46,579] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:46,583] [INFO] Selected 24 target genomes.
[2024-01-24 14:40:46,583] [INFO] Target genome list was writen to GCF_014202575.1_ASM1420257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:46,603] [INFO] Task started: fastANI
[2024-01-24 14:40:46,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cc71b4f-5a43-4905-b471-94aef15e0e05/GCF_014202575.1_ASM1420257v1_genomic.fna.gz --refList GCF_014202575.1_ASM1420257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202575.1_ASM1420257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:05,643] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:05,660] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:05,660] [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_014202575.1	s__Texcoconibacillus texcoconensis	100.0	1117	1119	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Texcoconibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003226325.1	s__Salipaludibacillus keqinensis	77.1761	52	1119	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_001866055.1	s__Anaerobacillus alkalidiazotrophicus	76.9814	53	1119	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111295.1	s__Salipaludibacillus aurantiacus	76.8448	54	1119	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_002335745.1	s__FJAT-44876 sp002335745	76.8354	82	1119	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_019042215.1	s__Evansella tamaricis	76.6484	65	1119	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_002019795.1	s__Bacillus_AO alkalicellulosilyticus	76.6172	53	1119	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_007830185.1	s__Bacillus_L nanhaiisediminis	76.5104	54	1119	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_000787375.1	s__Bacillus_L okhensis	76.4407	54	1119	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_004116265.1	s__Anaerobacillus alkaliphilus	76.2071	62	1119	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:05,662] [INFO] GTDB search result was written to GCF_014202575.1_ASM1420257v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:05,663] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:05,667] [INFO] DFAST_QC result json was written to GCF_014202575.1_ASM1420257v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:05,667] [INFO] DFAST_QC completed!
[2024-01-24 14:41:05,667] [INFO] Total running time: 0h1m20s