[2024-01-24 15:27:04,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:04,690] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:04,690] [INFO] DQC Reference Directory: /var/lib/cwl/stg6486c347-d5d7-4914-a9f6-b4a71cf51a16/dqc_reference
[2024-01-24 15:27:09,320] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:09,322] [INFO] Task started: Prodigal
[2024-01-24 15:27:09,323] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a553f80-08df-44cc-ac28-cee747eb6ac8/GCF_025994435.1_ASM2599443v1_genomic.fna.gz | prodigal -d GCF_025994435.1_ASM2599443v1_genomic.fna/cds.fna -a GCF_025994435.1_ASM2599443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:19,953] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:19,954] [INFO] Task started: HMMsearch
[2024-01-24 15:27:19,954] [INFO] Running command: hmmsearch --tblout GCF_025994435.1_ASM2599443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6486c347-d5d7-4914-a9f6-b4a71cf51a16/dqc_reference/reference_markers.hmm GCF_025994435.1_ASM2599443v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:20,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:20,266] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1a553f80-08df-44cc-ac28-cee747eb6ac8/GCF_025994435.1_ASM2599443v1_genomic.fna.gz]
[2024-01-24 15:27:20,311] [INFO] Query marker FASTA was written to GCF_025994435.1_ASM2599443v1_genomic.fna/markers.fasta
[2024-01-24 15:27:20,312] [INFO] Task started: Blastn
[2024-01-24 15:27:20,312] [INFO] Running command: blastn -query GCF_025994435.1_ASM2599443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6486c347-d5d7-4914-a9f6-b4a71cf51a16/dqc_reference/reference_markers.fasta -out GCF_025994435.1_ASM2599443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:21,245] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:21,249] [INFO] Selected 16 target genomes.
[2024-01-24 15:27:21,249] [INFO] Target genome list was writen to GCF_025994435.1_ASM2599443v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:21,293] [INFO] Task started: fastANI
[2024-01-24 15:27:21,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a553f80-08df-44cc-ac28-cee747eb6ac8/GCF_025994435.1_ASM2599443v1_genomic.fna.gz --refList GCF_025994435.1_ASM2599443v1_genomic.fna/target_genomes.txt --output GCF_025994435.1_ASM2599443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:34,253] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:34,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6486c347-d5d7-4914-a9f6-b4a71cf51a16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:34,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6486c347-d5d7-4914-a9f6-b4a71cf51a16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:34,268] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:34,268] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:34,269] [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
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	84.4917	761	1160	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	84.404	770	1160	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	84.3849	748	1160	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	82.313	674	1160	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	82.1459	661	1160	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	82.1443	643	1160	95	below_threshold
Novacetimonas cocois	strain=WE7	GCA_003311635.1	1747507	1747507	type	True	79.4637	452	1160	95	below_threshold
Komagataeibacter melomenusus	strain=AV436	GCA_013155395.1	2766578	2766578	type	True	79.4108	404	1160	95	below_threshold
Novacetimonas pomaceti	strain=T5K1	GCA_003207955.1	2021998	2021998	type	True	79.3853	447	1160	95	below_threshold
Novacetimonas hansenii	strain=JCM 7643	GCA_000964405.1	436	436	type	True	78.7533	331	1160	95	below_threshold
Novacetimonas hansenii	strain=NBRC 14820	GCA_006539705.1	436	436	type	True	78.7231	344	1160	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.1625	330	1160	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	76.7155	260	1160	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.7136	279	1160	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.6757	240	1160	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.367	246	1160	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:34,270] [INFO] DFAST Taxonomy check result was written to GCF_025994435.1_ASM2599443v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:34,271] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:34,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:34,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6486c347-d5d7-4914-a9f6-b4a71cf51a16/dqc_reference/checkm_data
[2024-01-24 15:27:34,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:34,313] [INFO] Task started: CheckM
[2024-01-24 15:27:34,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994435.1_ASM2599443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994435.1_ASM2599443v1_genomic.fna/checkm_input GCF_025994435.1_ASM2599443v1_genomic.fna/checkm_result
[2024-01-24 15:28:10,253] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:10,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:10,274] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:10,275] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:10,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994435.1_ASM2599443v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:10,276] [INFO] Task started: Blastn
[2024-01-24 15:28:10,276] [INFO] Running command: blastn -query GCF_025994435.1_ASM2599443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6486c347-d5d7-4914-a9f6-b4a71cf51a16/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994435.1_ASM2599443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:11,663] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:11,666] [INFO] Selected 8 target genomes.
[2024-01-24 15:28:11,666] [INFO] Target genome list was writen to GCF_025994435.1_ASM2599443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:11,676] [INFO] Task started: fastANI
[2024-01-24 15:28:11,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a553f80-08df-44cc-ac28-cee747eb6ac8/GCF_025994435.1_ASM2599443v1_genomic.fna.gz --refList GCF_025994435.1_ASM2599443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994435.1_ASM2599443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:19,379] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:19,387] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:19,387] [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_014174305.1	s__Gluconacetobacter johannae	99.9959	1149	1160	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014174355.1	s__Gluconacetobacter azotocaptans	93.2539	1019	1160	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCF_014174155.1	s__Gluconacetobacter tumulisoli	90.4405	892	1160	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	84.3916	771	1160	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	83.1621	697	1160	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174375.1	s__Gluconacetobacter asukensis	82.8432	712	1160	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	-
GCF_014174395.1	s__Gluconacetobacter aggeris	82.7177	685	1160	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_003311635.1	s__Komagataeibacter cocois	79.4749	451	1160	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	95.20	95.16	0.89	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:19,389] [INFO] GTDB search result was written to GCF_025994435.1_ASM2599443v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:19,390] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:19,394] [INFO] DFAST_QC result json was written to GCF_025994435.1_ASM2599443v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:19,395] [INFO] DFAST_QC completed!
[2024-01-24 15:28:19,395] [INFO] Total running time: 0h1m15s