[2024-01-24 13:22:40,411] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:40,413] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:40,413] [INFO] DQC Reference Directory: /var/lib/cwl/stgf74c1954-5d90-4230-9f6b-8edee2e4ec7e/dqc_reference
[2024-01-24 13:22:41,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:41,726] [INFO] Task started: Prodigal
[2024-01-24 13:22:41,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgd89be413-c9c9-4f4b-8d48-afbdff1f3be4/GCF_001721685.1_ASM172168v1_genomic.fna.gz | prodigal -d GCF_001721685.1_ASM172168v1_genomic.fna/cds.fna -a GCF_001721685.1_ASM172168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:51,885] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:51,886] [INFO] Task started: HMMsearch
[2024-01-24 13:22:51,886] [INFO] Running command: hmmsearch --tblout GCF_001721685.1_ASM172168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf74c1954-5d90-4230-9f6b-8edee2e4ec7e/dqc_reference/reference_markers.hmm GCF_001721685.1_ASM172168v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:52,146] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:52,147] [INFO] Found 6/6 markers.
[2024-01-24 13:22:52,179] [INFO] Query marker FASTA was written to GCF_001721685.1_ASM172168v1_genomic.fna/markers.fasta
[2024-01-24 13:22:52,179] [INFO] Task started: Blastn
[2024-01-24 13:22:52,179] [INFO] Running command: blastn -query GCF_001721685.1_ASM172168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf74c1954-5d90-4230-9f6b-8edee2e4ec7e/dqc_reference/reference_markers.fasta -out GCF_001721685.1_ASM172168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:52,830] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:52,833] [INFO] Selected 25 target genomes.
[2024-01-24 13:22:52,833] [INFO] Target genome list was writen to GCF_001721685.1_ASM172168v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:52,867] [INFO] Task started: fastANI
[2024-01-24 13:22:52,867] [INFO] Running command: fastANI --query /var/lib/cwl/stgd89be413-c9c9-4f4b-8d48-afbdff1f3be4/GCF_001721685.1_ASM172168v1_genomic.fna.gz --refList GCF_001721685.1_ASM172168v1_genomic.fna/target_genomes.txt --output GCF_001721685.1_ASM172168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:10,502] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:10,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf74c1954-5d90-4230-9f6b-8edee2e4ec7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:10,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf74c1954-5d90-4230-9f6b-8edee2e4ec7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:10,509] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:10,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:10,509] [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
Salisediminibacterium beveridgei	strain=MLTeJB	GCA_001721685.1	632773	632773	type	True	100.0	1193	1194	95	conclusive
Paenalkalicoccus suaedae	strain=M4U3P1	GCA_006965545.2	2592382	2592382	type	True	80.6787	50	1194	95	below_threshold
Salisediminibacterium selenitireducens	strain=MLS10	GCA_000093085.1	85683	85683	type	True	79.1249	309	1194	95	below_threshold
Salipaludibacillus aurantiacus	strain=S9	GCA_900111295.1	1601833	1601833	type	True	76.8681	67	1194	95	below_threshold
Alkalicoccus halolimnae	strain=BZ-SZ-XJ29	GCA_008014775.1	1667239	1667239	type	True	76.782	54	1194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:10,512] [INFO] DFAST Taxonomy check result was written to GCF_001721685.1_ASM172168v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:10,512] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:10,512] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:10,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf74c1954-5d90-4230-9f6b-8edee2e4ec7e/dqc_reference/checkm_data
[2024-01-24 13:23:10,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:10,555] [INFO] Task started: CheckM
[2024-01-24 13:23:10,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001721685.1_ASM172168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001721685.1_ASM172168v1_genomic.fna/checkm_input GCF_001721685.1_ASM172168v1_genomic.fna/checkm_result
[2024-01-24 13:23:45,153] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:45,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:45,172] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:45,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:45,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001721685.1_ASM172168v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:45,173] [INFO] Task started: Blastn
[2024-01-24 13:23:45,174] [INFO] Running command: blastn -query GCF_001721685.1_ASM172168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf74c1954-5d90-4230-9f6b-8edee2e4ec7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001721685.1_ASM172168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:45,913] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:45,917] [INFO] Selected 26 target genomes.
[2024-01-24 13:23:45,918] [INFO] Target genome list was writen to GCF_001721685.1_ASM172168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:45,967] [INFO] Task started: fastANI
[2024-01-24 13:23:45,967] [INFO] Running command: fastANI --query /var/lib/cwl/stgd89be413-c9c9-4f4b-8d48-afbdff1f3be4/GCF_001721685.1_ASM172168v1_genomic.fna.gz --refList GCF_001721685.1_ASM172168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001721685.1_ASM172168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:03,822] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:03,831] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:03,831] [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_001721685.1	s__Salisediminibacterium beveridgei	100.0	1193	1194	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salisediminibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006965545.2	s__Alkalicoccus sp006965545	81.1008	51	1194	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000093085.1	s__Salisediminibacterium selenitireducens	79.1337	309	1194	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salisediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111295.1	s__Salipaludibacillus aurantiacus	76.8681	67	1194	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_008014775.1	s__Alkalicoccus halolimnae	76.7464	53	1194	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:03,833] [INFO] GTDB search result was written to GCF_001721685.1_ASM172168v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:03,834] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:03,837] [INFO] DFAST_QC result json was written to GCF_001721685.1_ASM172168v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:03,837] [INFO] DFAST_QC completed!
[2024-01-24 13:24:03,837] [INFO] Total running time: 0h1m23s