[2024-01-24 11:52:04,700] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg2aedc388-775e-45bd-b889-352cf86a7fc9/dqc_reference
[2024-01-24 11:52:05,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:05,926] [INFO] Task started: Prodigal
[2024-01-24 11:52:05,926] [INFO] Running command: gunzip -c /var/lib/cwl/stg3be8c1cf-25d6-46bc-8444-d8d0c42637c7/GCF_025995595.1_ASM2599559v1_genomic.fna.gz | prodigal -d GCF_025995595.1_ASM2599559v1_genomic.fna/cds.fna -a GCF_025995595.1_ASM2599559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:16,244] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:16,245] [INFO] Task started: HMMsearch
[2024-01-24 11:52:16,245] [INFO] Running command: hmmsearch --tblout GCF_025995595.1_ASM2599559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2aedc388-775e-45bd-b889-352cf86a7fc9/dqc_reference/reference_markers.hmm GCF_025995595.1_ASM2599559v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:16,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:16,502] [INFO] Found 6/6 markers.
[2024-01-24 11:52:16,543] [INFO] Query marker FASTA was written to GCF_025995595.1_ASM2599559v1_genomic.fna/markers.fasta
[2024-01-24 11:52:16,543] [INFO] Task started: Blastn
[2024-01-24 11:52:16,544] [INFO] Running command: blastn -query GCF_025995595.1_ASM2599559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2aedc388-775e-45bd-b889-352cf86a7fc9/dqc_reference/reference_markers.fasta -out GCF_025995595.1_ASM2599559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:17,267] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:17,272] [INFO] Selected 16 target genomes.
[2024-01-24 11:52:17,272] [INFO] Target genome list was writen to GCF_025995595.1_ASM2599559v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:17,308] [INFO] Task started: fastANI
[2024-01-24 11:52:17,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg3be8c1cf-25d6-46bc-8444-d8d0c42637c7/GCF_025995595.1_ASM2599559v1_genomic.fna.gz --refList GCF_025995595.1_ASM2599559v1_genomic.fna/target_genomes.txt --output GCF_025995595.1_ASM2599559v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:26,963] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:26,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2aedc388-775e-45bd-b889-352cf86a7fc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:26,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2aedc388-775e-45bd-b889-352cf86a7fc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:26,986] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:52:26,987] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:26,987] [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
Acetobacter oeni	strain=LMG 21952	GCA_011516825.1	304077	304077	type	True	99.9972	1246	1251	95	conclusive
Acetobacter oeni	strain=DSM 23926	GCA_014196315.1	304077	304077	type	True	99.9939	1245	1251	95	conclusive
Acetobacter fallax	strain=LMG 1636	GCA_011516735.1	1737473	1737473	type	True	81.8401	664	1251	95	below_threshold
Acetobacter conturbans	strain=LMG 1627	GCA_011516755.1	1737472	1737472	type	True	80.7451	275	1251	95	below_threshold
Acetobacter estunensis	strain=LMG 1626	GCA_011516945.1	104097	104097	type	True	80.4545	241	1251	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	80.2871	145	1251	95	below_threshold
Acetobacter aceti	strain=NBRC 14818	GCA_000193495.2	435	435	type	True	79.9942	254	1251	95	below_threshold
Acetobacter aceti	strain=DSM 3508	GCA_004341595.1	435	435	type	True	79.8875	250	1251	95	below_threshold
Acetobacter nitrogenifigens	strain=NBRC 105050	GCA_007991375.1	285268	285268	type	True	78.1298	221	1251	95	below_threshold
Acetobacter nitrogenifigens	strain=DSM 23921	GCA_000429165.1	285268	285268	type	True	78.0118	231	1251	95	below_threshold
Gluconobacter albidus	strain=NBRC 3250	GCA_002723915.1	318683	318683	type	True	77.4652	83	1251	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.3951	112	1251	95	below_threshold
Gluconobacter frateurii	strain=NBRC 3264	GCA_002723955.1	38308	38308	suspected-type	True	77.2261	66	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:26,988] [INFO] DFAST Taxonomy check result was written to GCF_025995595.1_ASM2599559v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:26,989] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:26,989] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:26,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2aedc388-775e-45bd-b889-352cf86a7fc9/dqc_reference/checkm_data
[2024-01-24 11:52:26,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:27,035] [INFO] Task started: CheckM
[2024-01-24 11:52:27,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995595.1_ASM2599559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995595.1_ASM2599559v1_genomic.fna/checkm_input GCF_025995595.1_ASM2599559v1_genomic.fna/checkm_result
[2024-01-24 11:53:01,811] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:01,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:01,837] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:01,837] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:01,837] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995595.1_ASM2599559v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:01,838] [INFO] Task started: Blastn
[2024-01-24 11:53:01,838] [INFO] Running command: blastn -query GCF_025995595.1_ASM2599559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2aedc388-775e-45bd-b889-352cf86a7fc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995595.1_ASM2599559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:03,054] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:03,058] [INFO] Selected 16 target genomes.
[2024-01-24 11:53:03,058] [INFO] Target genome list was writen to GCF_025995595.1_ASM2599559v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:03,091] [INFO] Task started: fastANI
[2024-01-24 11:53:03,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg3be8c1cf-25d6-46bc-8444-d8d0c42637c7/GCF_025995595.1_ASM2599559v1_genomic.fna.gz --refList GCF_025995595.1_ASM2599559v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995595.1_ASM2599559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:13,241] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:13,256] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:13,256] [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_011516825.1	s__Acetobacter oeni	99.9972	1246	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_011516835.1	s__Acetobacter musti	82.2142	666	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516735.1	s__Acetobacter fallax	81.8452	662	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011516765.1	s__Acetobacter sicerae	81.787	293	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516755.1	s__Acetobacter conturbans	80.7552	275	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516945.1	s__Acetobacter estunensis	80.4545	241	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000193495.2	s__Acetobacter aceti	79.993	252	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.82	96.47	0.96	0.89	7	-
GCF_002005445.1	s__Acetobacter aceti_B	79.2883	247	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019083805.1	s__Acetobacter estunensis_A	79.0814	209	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017377715.1	s__Acetobacter sacchari	78.0835	218	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429165.1	s__Acetobacter nitrogenifigens	78.0268	230	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002153745.1	s__Acetobacter sp002153745	77.6423	136	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723915.1	s__Gluconobacter albidus	77.4652	83	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_009547075.1	s__Gluconobacter sp009547075	77.3751	112	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723955.1	s__Gluconobacter_A frateurii	77.2261	66	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	97.06	97.06	0.93	0.93	2	-
GCA_012517935.1	s__Acetobacter sp012517935	77.1479	93	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:13,258] [INFO] GTDB search result was written to GCF_025995595.1_ASM2599559v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:13,259] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:13,262] [INFO] DFAST_QC result json was written to GCF_025995595.1_ASM2599559v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:13,263] [INFO] DFAST_QC completed!
[2024-01-24 11:53:13,263] [INFO] Total running time: 0h1m9s