[2024-01-24 11:26:20,763] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,765] [INFO] DQC Reference Directory: /var/lib/cwl/stg408e8a58-885e-41f6-a6df-0a18f4d5f722/dqc_reference
[2024-01-24 11:26:21,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:21,956] [INFO] Task started: Prodigal
[2024-01-24 11:26:21,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c47ffb0-25e3-47ca-bd3d-8ea20a38eabe/GCF_006538165.1_ASM653816v1_genomic.fna.gz | prodigal -d GCF_006538165.1_ASM653816v1_genomic.fna/cds.fna -a GCF_006538165.1_ASM653816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:34,001] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:34,001] [INFO] Task started: HMMsearch
[2024-01-24 11:26:34,002] [INFO] Running command: hmmsearch --tblout GCF_006538165.1_ASM653816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg408e8a58-885e-41f6-a6df-0a18f4d5f722/dqc_reference/reference_markers.hmm GCF_006538165.1_ASM653816v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:34,302] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:34,304] [INFO] Found 6/6 markers.
[2024-01-24 11:26:34,337] [INFO] Query marker FASTA was written to GCF_006538165.1_ASM653816v1_genomic.fna/markers.fasta
[2024-01-24 11:26:34,338] [INFO] Task started: Blastn
[2024-01-24 11:26:34,338] [INFO] Running command: blastn -query GCF_006538165.1_ASM653816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg408e8a58-885e-41f6-a6df-0a18f4d5f722/dqc_reference/reference_markers.fasta -out GCF_006538165.1_ASM653816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:35,138] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:35,142] [INFO] Selected 10 target genomes.
[2024-01-24 11:26:35,143] [INFO] Target genome list was writen to GCF_006538165.1_ASM653816v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:35,147] [INFO] Task started: fastANI
[2024-01-24 11:26:35,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c47ffb0-25e3-47ca-bd3d-8ea20a38eabe/GCF_006538165.1_ASM653816v1_genomic.fna.gz --refList GCF_006538165.1_ASM653816v1_genomic.fna/target_genomes.txt --output GCF_006538165.1_ASM653816v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:43,496] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:43,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg408e8a58-885e-41f6-a6df-0a18f4d5f722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:43,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg408e8a58-885e-41f6-a6df-0a18f4d5f722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:43,523] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:43,523] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:43,523] [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
Komagataeibacter diospyri	strain=MSKU 9	GCA_006538165.1	1932662	1932662	type	True	100.0	1196	1203	95	conclusive
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	91.0966	956	1203	95	below_threshold
Komagataeibacter europaeus	strain=type strain:LMG 18890	GCA_000285295.1	33995	33995	suspected-type	True	90.7687	947	1203	95	below_threshold
Komagataeibacter intermedius	strain=TF2	GCA_000964425.1	66229	66229	type	True	88.7445	857	1203	95	below_threshold
Komagataeibacter oboediens	strain=LMG 18849	GCA_003207815.1	65958	65958	type	True	88.5864	862	1203	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.8963	332	1203	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.8765	164	1203	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.6178	124	1203	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	75.6801	59	1203	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:43,525] [INFO] DFAST Taxonomy check result was written to GCF_006538165.1_ASM653816v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:43,526] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:43,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:43,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg408e8a58-885e-41f6-a6df-0a18f4d5f722/dqc_reference/checkm_data
[2024-01-24 11:26:43,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:43,571] [INFO] Task started: CheckM
[2024-01-24 11:26:43,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006538165.1_ASM653816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006538165.1_ASM653816v1_genomic.fna/checkm_input GCF_006538165.1_ASM653816v1_genomic.fna/checkm_result
[2024-01-24 11:27:21,931] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:21,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:21,955] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:21,956] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:21,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006538165.1_ASM653816v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:21,957] [INFO] Task started: Blastn
[2024-01-24 11:27:21,957] [INFO] Running command: blastn -query GCF_006538165.1_ASM653816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg408e8a58-885e-41f6-a6df-0a18f4d5f722/dqc_reference/reference_markers_gtdb.fasta -out GCF_006538165.1_ASM653816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:23,341] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:23,344] [INFO] Selected 7 target genomes.
[2024-01-24 11:27:23,344] [INFO] Target genome list was writen to GCF_006538165.1_ASM653816v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:23,350] [INFO] Task started: fastANI
[2024-01-24 11:27:23,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c47ffb0-25e3-47ca-bd3d-8ea20a38eabe/GCF_006538165.1_ASM653816v1_genomic.fna.gz --refList GCF_006538165.1_ASM653816v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006538165.1_ASM653816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:29,957] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:29,971] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:29,972] [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_006538165.1	s__Komagataeibacter diospyri	100.0	1196	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.62	98.62	0.92	0.92	2	conclusive
GCF_003207895.1	s__Komagataeibacter swingsii	91.0779	957	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	96.10	95.69	0.87	0.84	5	-
GCF_000285295.1	s__Komagataeibacter europaeus	90.7641	948	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	97.91	97.46	0.85	0.81	8	-
GCF_015155755.1	s__Komagataeibacter sp015155755	90.7187	908	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964425.1	s__Komagataeibacter intermedius	88.7682	855	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.80	99.80	0.96	0.96	2	-
GCF_003207815.1	s__Komagataeibacter oboediens	88.6024	861	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.65	98.22	0.88	0.85	10	-
GCF_000182745.2	s__Komagataeibacter medellinensis	84.2529	771	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.49	98.49	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:29,973] [INFO] GTDB search result was written to GCF_006538165.1_ASM653816v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:29,974] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:29,977] [INFO] DFAST_QC result json was written to GCF_006538165.1_ASM653816v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:29,978] [INFO] DFAST_QC completed!
[2024-01-24 11:27:29,978] [INFO] Total running time: 0h1m9s