[2024-01-24 10:49:33,816] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:33,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:33,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg37deff1a-55e7-4382-9291-0edd1d4eb056/dqc_reference
[2024-01-24 10:49:35,075] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:35,076] [INFO] Task started: Prodigal
[2024-01-24 10:49:35,076] [INFO] Running command: gunzip -c /var/lib/cwl/stga610b37e-2ac4-4699-b49f-39431e2ea685/GCF_014048465.1_ASM1404846v1_genomic.fna.gz | prodigal -d GCF_014048465.1_ASM1404846v1_genomic.fna/cds.fna -a GCF_014048465.1_ASM1404846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:41,408] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:41,408] [INFO] Task started: HMMsearch
[2024-01-24 10:49:41,408] [INFO] Running command: hmmsearch --tblout GCF_014048465.1_ASM1404846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37deff1a-55e7-4382-9291-0edd1d4eb056/dqc_reference/reference_markers.hmm GCF_014048465.1_ASM1404846v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:41,650] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:41,652] [INFO] Found 6/6 markers.
[2024-01-24 10:49:41,675] [INFO] Query marker FASTA was written to GCF_014048465.1_ASM1404846v1_genomic.fna/markers.fasta
[2024-01-24 10:49:41,675] [INFO] Task started: Blastn
[2024-01-24 10:49:41,675] [INFO] Running command: blastn -query GCF_014048465.1_ASM1404846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37deff1a-55e7-4382-9291-0edd1d4eb056/dqc_reference/reference_markers.fasta -out GCF_014048465.1_ASM1404846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:42,468] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:42,472] [INFO] Selected 17 target genomes.
[2024-01-24 10:49:42,473] [INFO] Target genome list was writen to GCF_014048465.1_ASM1404846v1_genomic.fna/target_genomes.txt
[2024-01-24 10:49:42,481] [INFO] Task started: fastANI
[2024-01-24 10:49:42,481] [INFO] Running command: fastANI --query /var/lib/cwl/stga610b37e-2ac4-4699-b49f-39431e2ea685/GCF_014048465.1_ASM1404846v1_genomic.fna.gz --refList GCF_014048465.1_ASM1404846v1_genomic.fna/target_genomes.txt --output GCF_014048465.1_ASM1404846v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:50,797] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:50,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37deff1a-55e7-4382-9291-0edd1d4eb056/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:50,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37deff1a-55e7-4382-9291-0edd1d4eb056/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:50,811] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:49:50,812] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:49:50,812] [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
Bombella apis	strain=MRM1	GCA_014878255.1	1785988	1785988	type	True	87.9595	579	684	95	below_threshold
Bombella apis	strain=MRM1	GCA_018221685.1	1785988	1785988	type	True	87.8443	572	684	95	below_threshold
Bombella favorum	strain=TMW 2.1880	GCA_014048475.1	2039164	2039164	type	True	82.7203	482	684	95	below_threshold
Bombella intestini	strain=R-52487	GCA_002003665.1	1539051	1539051	type	True	82.3175	497	684	95	below_threshold
Gluconobacter japonicus	strain=NBRC 3271	GCA_002723975.1	376620	376620	type	True	77.5041	94	684	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	77.3653	143	684	95	below_threshold
Gluconobacter roseus	strain=NBRC 3990	GCA_006538885.1	586239	586239	type	True	77.3467	141	684	95	below_threshold
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	77.2899	146	684	95	below_threshold
Komagataeibacter melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	77.0732	112	684	95	below_threshold
Komagataeibacter diospyri	strain=MSKU 9	GCA_006538165.1	1932662	1932662	type	True	77.0035	101	684	95	below_threshold
Tanticharoenia sakaeratensis	strain=NBRC 103193	GCA_000963885.1	444053	444053	type	True	77.0031	86	684	95	below_threshold
Acidomonas methanolica	strain=NBRC 104435	GCA_007988925.1	437	437	type	True	76.9369	111	684	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	76.811	88	684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:50,814] [INFO] DFAST Taxonomy check result was written to GCF_014048465.1_ASM1404846v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:50,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:50,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:50,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37deff1a-55e7-4382-9291-0edd1d4eb056/dqc_reference/checkm_data
[2024-01-24 10:49:50,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:50,844] [INFO] Task started: CheckM
[2024-01-24 10:49:50,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014048465.1_ASM1404846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014048465.1_ASM1404846v1_genomic.fna/checkm_input GCF_014048465.1_ASM1404846v1_genomic.fna/checkm_result
[2024-01-24 10:50:26,693] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:26,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:26,720] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:26,720] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:26,721] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014048465.1_ASM1404846v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:26,721] [INFO] Task started: Blastn
[2024-01-24 10:50:26,721] [INFO] Running command: blastn -query GCF_014048465.1_ASM1404846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37deff1a-55e7-4382-9291-0edd1d4eb056/dqc_reference/reference_markers_gtdb.fasta -out GCF_014048465.1_ASM1404846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:28,076] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:28,081] [INFO] Selected 11 target genomes.
[2024-01-24 10:50:28,082] [INFO] Target genome list was writen to GCF_014048465.1_ASM1404846v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:28,110] [INFO] Task started: fastANI
[2024-01-24 10:50:28,111] [INFO] Running command: fastANI --query /var/lib/cwl/stga610b37e-2ac4-4699-b49f-39431e2ea685/GCF_014048465.1_ASM1404846v1_genomic.fna.gz --refList GCF_014048465.1_ASM1404846v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014048465.1_ASM1404846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:33,668] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:33,677] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:33,677] [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_014048465.1	s__Bombella mellum	100.0	683	684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018221685.1	s__Bombella apis	87.8443	572	684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.16	98.65	0.96	0.94	13	-
GCF_014048475.1	s__Bombella favorum	82.7205	481	684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002003665.1	s__Bombella intestini	82.3175	497	684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725755.1	s__Bombella sp009725755	78.7954	216	684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.22	99.22	0.99	0.99	2	-
GCF_002592045.1	s__Bombella apium_A	78.6039	206	684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403295.1	s__Komagataeibacter melaceti	77.0732	112	684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538165.1	s__Komagataeibacter diospyri	77.0035	101	684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.62	98.62	0.92	0.92	2	-
GCF_000963885.1	s__Tanticharoenia sakaeratensis	77.0004	87	684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Tanticharoenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346035.1	s__Acidomonas methanolica	76.9252	114	684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:33,679] [INFO] GTDB search result was written to GCF_014048465.1_ASM1404846v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:33,681] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:33,686] [INFO] DFAST_QC result json was written to GCF_014048465.1_ASM1404846v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:33,686] [INFO] DFAST_QC completed!
[2024-01-24 10:50:33,686] [INFO] Total running time: 0h0m60s