[2024-01-24 11:13:04,567] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg61f85bd4-06a1-47ce-974d-cc6b42445066/dqc_reference
[2024-01-24 11:13:05,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,809] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,809] [INFO] Running command: gunzip -c /var/lib/cwl/stga70cd812-2781-49ca-a81e-c5a537618e1f/GCF_023895975.1_ASM2389597v1_genomic.fna.gz | prodigal -d GCF_023895975.1_ASM2389597v1_genomic.fna/cds.fna -a GCF_023895975.1_ASM2389597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:17,490] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:17,491] [INFO] Task started: HMMsearch
[2024-01-24 11:13:17,491] [INFO] Running command: hmmsearch --tblout GCF_023895975.1_ASM2389597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61f85bd4-06a1-47ce-974d-cc6b42445066/dqc_reference/reference_markers.hmm GCF_023895975.1_ASM2389597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:17,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:17,855] [INFO] Found 6/6 markers.
[2024-01-24 11:13:17,898] [INFO] Query marker FASTA was written to GCF_023895975.1_ASM2389597v1_genomic.fna/markers.fasta
[2024-01-24 11:13:17,899] [INFO] Task started: Blastn
[2024-01-24 11:13:17,899] [INFO] Running command: blastn -query GCF_023895975.1_ASM2389597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61f85bd4-06a1-47ce-974d-cc6b42445066/dqc_reference/reference_markers.fasta -out GCF_023895975.1_ASM2389597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:18,647] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:18,652] [INFO] Selected 17 target genomes.
[2024-01-24 11:13:18,653] [INFO] Target genome list was writen to GCF_023895975.1_ASM2389597v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:18,675] [INFO] Task started: fastANI
[2024-01-24 11:13:18,676] [INFO] Running command: fastANI --query /var/lib/cwl/stga70cd812-2781-49ca-a81e-c5a537618e1f/GCF_023895975.1_ASM2389597v1_genomic.fna.gz --refList GCF_023895975.1_ASM2389597v1_genomic.fna/target_genomes.txt --output GCF_023895975.1_ASM2389597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:30,455] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:30,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61f85bd4-06a1-47ce-974d-cc6b42445066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:30,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61f85bd4-06a1-47ce-974d-cc6b42445066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:30,479] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:30,479] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:30,480] [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
Microbulbifer variabilis	strain=ATCC 700307	GCA_000380565.1	266805	266805	type	True	80.0736	591	1473	95	below_threshold
Microbulbifer marinus	strain=CGMCC 1.10657	GCA_900107725.1	658218	658218	type	True	78.8967	297	1473	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	78.6808	318	1473	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	78.543	298	1473	95	below_threshold
Microbulbifer flavimaris	strain=WRN-8	GCA_001641755.2	1781068	1781068	type	True	78.4955	230	1473	95	below_threshold
Microbulbifer hydrolyticus	strain=IRE-31	GCA_009931115.1	48074	48074	type	True	78.4661	189	1473	95	below_threshold
Microbulbifer hydrolyticus	strain=DSM 11525	GCA_014202835.1	48074	48074	type	True	78.4306	190	1473	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	78.2417	270	1473	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	78.2004	190	1473	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	78.1416	190	1473	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	78.1058	191	1473	95	below_threshold
Microbulbifer rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	78.074	245	1473	95	below_threshold
Marinimicrobium koreense	strain=DSM 16974	GCA_003762925.1	306545	306545	type	True	76.964	60	1473	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.8926	53	1473	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:30,496] [INFO] DFAST Taxonomy check result was written to GCF_023895975.1_ASM2389597v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:30,497] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:30,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:30,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61f85bd4-06a1-47ce-974d-cc6b42445066/dqc_reference/checkm_data
[2024-01-24 11:13:30,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:30,551] [INFO] Task started: CheckM
[2024-01-24 11:13:30,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023895975.1_ASM2389597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023895975.1_ASM2389597v1_genomic.fna/checkm_input GCF_023895975.1_ASM2389597v1_genomic.fna/checkm_result
[2024-01-24 11:14:09,291] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:09,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:09,316] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:09,316] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:09,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023895975.1_ASM2389597v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:09,317] [INFO] Task started: Blastn
[2024-01-24 11:14:09,317] [INFO] Running command: blastn -query GCF_023895975.1_ASM2389597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61f85bd4-06a1-47ce-974d-cc6b42445066/dqc_reference/reference_markers_gtdb.fasta -out GCF_023895975.1_ASM2389597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:10,516] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:10,520] [INFO] Selected 10 target genomes.
[2024-01-24 11:14:10,520] [INFO] Target genome list was writen to GCF_023895975.1_ASM2389597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:10,546] [INFO] Task started: fastANI
[2024-01-24 11:14:10,546] [INFO] Running command: fastANI --query /var/lib/cwl/stga70cd812-2781-49ca-a81e-c5a537618e1f/GCF_023895975.1_ASM2389597v1_genomic.fna.gz --refList GCF_023895975.1_ASM2389597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023895975.1_ASM2389597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:19,486] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:19,496] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:14:19,496] [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_003076275.1	s__Microbulbifer sp003076275	81.5236	793	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007183175.1	s__Microbulbifer sp007183175	80.4002	633	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380565.1	s__Microbulbifer variabilis	80.0533	593	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363535.1	s__Microbulbifer sp009363535	80.0172	606	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107725.1	s__Microbulbifer marinus	78.919	297	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129095.1	s__Microbulbifer donghaiensis	78.6678	319	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931115.1	s__Microbulbifer hydrolyticus	78.4871	188	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013367775.1	s__Microbulbifer sp013367775	78.3162	223	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904735.1	s__Microbulbifer hainanensis	78.2555	269	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:19,501] [INFO] GTDB search result was written to GCF_023895975.1_ASM2389597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:19,502] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:19,506] [INFO] DFAST_QC result json was written to GCF_023895975.1_ASM2389597v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:19,507] [INFO] DFAST_QC completed!
[2024-01-24 11:14:19,507] [INFO] Total running time: 0h1m15s