[2024-01-24 13:56:13,226] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:13,228] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:13,228] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c5849ac-b78f-4ee2-a967-3999b4b93810/dqc_reference
[2024-01-24 13:56:14,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,532] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg71f4a014-c7ed-4b12-8221-5ce02437a7be/GCF_020884775.1_ASM2088477v1_genomic.fna.gz | prodigal -d GCF_020884775.1_ASM2088477v1_genomic.fna/cds.fna -a GCF_020884775.1_ASM2088477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:22,858] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:22,859] [INFO] Task started: HMMsearch
[2024-01-24 13:56:22,859] [INFO] Running command: hmmsearch --tblout GCF_020884775.1_ASM2088477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c5849ac-b78f-4ee2-a967-3999b4b93810/dqc_reference/reference_markers.hmm GCF_020884775.1_ASM2088477v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:23,139] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:23,141] [INFO] Found 6/6 markers.
[2024-01-24 13:56:23,171] [INFO] Query marker FASTA was written to GCF_020884775.1_ASM2088477v1_genomic.fna/markers.fasta
[2024-01-24 13:56:23,172] [INFO] Task started: Blastn
[2024-01-24 13:56:23,172] [INFO] Running command: blastn -query GCF_020884775.1_ASM2088477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c5849ac-b78f-4ee2-a967-3999b4b93810/dqc_reference/reference_markers.fasta -out GCF_020884775.1_ASM2088477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:23,907] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:23,912] [INFO] Selected 15 target genomes.
[2024-01-24 13:56:23,912] [INFO] Target genome list was writen to GCF_020884775.1_ASM2088477v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:23,920] [INFO] Task started: fastANI
[2024-01-24 13:56:23,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f4a014-c7ed-4b12-8221-5ce02437a7be/GCF_020884775.1_ASM2088477v1_genomic.fna.gz --refList GCF_020884775.1_ASM2088477v1_genomic.fna/target_genomes.txt --output GCF_020884775.1_ASM2088477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:33,592] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:33,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c5849ac-b78f-4ee2-a967-3999b4b93810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:33,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c5849ac-b78f-4ee2-a967-3999b4b93810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:33,606] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:56:33,607] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:33,607] [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
Gluconobacter wancherniae	strain=NBRC 103581	GCA_020884775.1	1307955	1307955	type	True	100.0	925	925	95	conclusive
Gluconobacter wancherniae	strain=LMG27016	GCA_015244585.1	1307955	1307955	type	True	99.9994	923	925	95	conclusive
Gluconobacter wancherniae	strain=NBRC 103581	GCA_007988885.1	1307955	1307955	type	True	99.9976	925	925	95	conclusive
Gluconobacter albidus	strain=NBRC 3250	GCA_002723915.1	318683	318683	type	True	79.3945	296	925	95	below_threshold
Gluconobacter japonicus	strain=NBRC 3271	GCA_002723975.1	376620	376620	type	True	78.8133	285	925	95	below_threshold
Gluconobacter frateurii	strain=NBRC 3264	GCA_002723955.1	38308	38308	suspected-type	True	78.6096	293	925	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	78.605	279	925	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	78.4672	294	925	95	below_threshold
Gluconobacter vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	78.33	284	925	95	below_threshold
Gluconobacter morbifer	strain=G707	GCA_000234355.2	479935	479935	type	True	77.9246	239	925	95	below_threshold
Acidomonas methanolica	strain=NBRC 104435	GCA_007988925.1	437	437	type	True	76.7988	98	925	95	below_threshold
Acidomonas methanolica	strain=MB58	GCA_000617865.1	437	437	type	True	76.7743	99	925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:33,608] [INFO] DFAST Taxonomy check result was written to GCF_020884775.1_ASM2088477v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:33,609] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:33,609] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:33,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c5849ac-b78f-4ee2-a967-3999b4b93810/dqc_reference/checkm_data
[2024-01-24 13:56:33,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:33,638] [INFO] Task started: CheckM
[2024-01-24 13:56:33,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020884775.1_ASM2088477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020884775.1_ASM2088477v1_genomic.fna/checkm_input GCF_020884775.1_ASM2088477v1_genomic.fna/checkm_result
[2024-01-24 13:57:04,152] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:04,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:04,182] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:04,183] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:04,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020884775.1_ASM2088477v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:04,184] [INFO] Task started: Blastn
[2024-01-24 13:57:04,184] [INFO] Running command: blastn -query GCF_020884775.1_ASM2088477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c5849ac-b78f-4ee2-a967-3999b4b93810/dqc_reference/reference_markers_gtdb.fasta -out GCF_020884775.1_ASM2088477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:05,445] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:05,449] [INFO] Selected 20 target genomes.
[2024-01-24 13:57:05,450] [INFO] Target genome list was writen to GCF_020884775.1_ASM2088477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:05,474] [INFO] Task started: fastANI
[2024-01-24 13:57:05,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f4a014-c7ed-4b12-8221-5ce02437a7be/GCF_020884775.1_ASM2088477v1_genomic.fna.gz --refList GCF_020884775.1_ASM2088477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020884775.1_ASM2088477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:18,113] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:18,131] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:18,132] [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_007988885.1	s__Gluconobacter_B wancherniae	99.9976	925	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_B	95.0	99.01	98.51	0.95	0.90	4	conclusive
GCF_002723915.1	s__Gluconobacter albidus	79.3982	295	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_002723975.1	s__Gluconobacter_A japonicus	78.795	285	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	96.84	95.27	0.89	0.85	9	-
GCF_002723935.1	s__Gluconobacter_A cerinus	78.7749	283	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	96.40	95.61	0.88	0.86	20	-
GCF_000964465.1	s__Gluconobacter_A thailandicus	78.7406	281	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	98.77	97.43	0.93	0.88	11	-
GCF_015244675.1	s__Gluconobacter cerevisiae	78.73	273	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_018811945.1	s__Gluconobacter sp018811945	78.6755	281	925	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	78.6169	291	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	97.06	97.06	0.93	0.93	2	-
GCF_009547075.1	s__Gluconobacter sp009547075	78.5966	279	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580675.1	s__Gluconobacter potus	78.3718	285	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.92	96.89	0.82	0.80	7	-
GCF_014132155.1	s__Gluconobacter_A sp014132155	78.3545	268	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	97.46	96.68	0.90	0.89	4	-
GCF_015244565.1	s__Gluconobacter vitians	78.33	284	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539685.1	s__Gluconobacter oxydans	78.3107	277	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	-
GCF_000234355.1	s__Gluconobacter_C morbifer	77.922	237	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221685.1	s__Bombella apis	76.9647	78	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.16	98.65	0.96	0.94	13	-
GCF_004346035.1	s__Acidomonas methanolica	76.9153	101	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
GCF_002153605.1	s__Acetobacter malorum_A	76.4724	71	925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.53	96.53	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:18,133] [INFO] GTDB search result was written to GCF_020884775.1_ASM2088477v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:18,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:18,138] [INFO] DFAST_QC result json was written to GCF_020884775.1_ASM2088477v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:18,138] [INFO] DFAST_QC completed!
[2024-01-24 13:57:18,138] [INFO] Total running time: 0h1m5s