[2024-01-24 13:12:38,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,942] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,943] [INFO] DQC Reference Directory: /var/lib/cwl/stg804f1cf2-2de8-44ad-936e-24bd108975db/dqc_reference
[2024-01-24 13:12:40,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,281] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg52e6d4af-aa11-4f6e-a456-e92171af8728/GCF_949281285.1_ASM94928128v1_genomic.fna.gz | prodigal -d GCF_949281285.1_ASM94928128v1_genomic.fna/cds.fna -a GCF_949281285.1_ASM94928128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:53,007] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:53,007] [INFO] Task started: HMMsearch
[2024-01-24 13:12:53,007] [INFO] Running command: hmmsearch --tblout GCF_949281285.1_ASM94928128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg804f1cf2-2de8-44ad-936e-24bd108975db/dqc_reference/reference_markers.hmm GCF_949281285.1_ASM94928128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:53,377] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:53,381] [INFO] Found 6/6 markers.
[2024-01-24 13:12:53,433] [INFO] Query marker FASTA was written to GCF_949281285.1_ASM94928128v1_genomic.fna/markers.fasta
[2024-01-24 13:12:53,434] [INFO] Task started: Blastn
[2024-01-24 13:12:53,434] [INFO] Running command: blastn -query GCF_949281285.1_ASM94928128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg804f1cf2-2de8-44ad-936e-24bd108975db/dqc_reference/reference_markers.fasta -out GCF_949281285.1_ASM94928128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:54,316] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:54,319] [INFO] Selected 11 target genomes.
[2024-01-24 13:12:54,319] [INFO] Target genome list was writen to GCF_949281285.1_ASM94928128v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:54,324] [INFO] Task started: fastANI
[2024-01-24 13:12:54,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg52e6d4af-aa11-4f6e-a456-e92171af8728/GCF_949281285.1_ASM94928128v1_genomic.fna.gz --refList GCF_949281285.1_ASM94928128v1_genomic.fna/target_genomes.txt --output GCF_949281285.1_ASM94928128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:05,262] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:05,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg804f1cf2-2de8-44ad-936e-24bd108975db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:05,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg804f1cf2-2de8-44ad-936e-24bd108975db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:05,272] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:05,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:05,273] [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 intermedius	strain=TF2	GCA_000964425.1	66229	66229	type	True	99.8912	1093	1213	95	conclusive
Komagataeibacter oboediens	strain=LMG 18849	GCA_003207815.1	65958	65958	type	True	94.3833	958	1213	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	89.7208	893	1213	95	below_threshold
Komagataeibacter europaeus	strain=type strain:LMG 18890	GCA_000285295.1	33995	33995	suspected-type	True	89.6888	903	1213	95	below_threshold
Komagataeibacter diospyri	strain=MSKU 9	GCA_006538165.1	1932662	1932662	type	True	88.948	891	1213	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.3583	146	1213	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.5246	144	1213	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.4726	89	1213	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.8798	53	1213	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	75.6159	79	1213	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:05,274] [INFO] DFAST Taxonomy check result was written to GCF_949281285.1_ASM94928128v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:05,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:05,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:05,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg804f1cf2-2de8-44ad-936e-24bd108975db/dqc_reference/checkm_data
[2024-01-24 13:13:05,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:05,316] [INFO] Task started: CheckM
[2024-01-24 13:13:05,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_949281285.1_ASM94928128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_949281285.1_ASM94928128v1_genomic.fna/checkm_input GCF_949281285.1_ASM94928128v1_genomic.fna/checkm_result
[2024-01-24 13:13:46,664] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:46,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:46,685] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:46,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:46,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_949281285.1_ASM94928128v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:46,687] [INFO] Task started: Blastn
[2024-01-24 13:13:46,687] [INFO] Running command: blastn -query GCF_949281285.1_ASM94928128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg804f1cf2-2de8-44ad-936e-24bd108975db/dqc_reference/reference_markers_gtdb.fasta -out GCF_949281285.1_ASM94928128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:47,870] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:47,875] [INFO] Selected 11 target genomes.
[2024-01-24 13:13:47,875] [INFO] Target genome list was writen to GCF_949281285.1_ASM94928128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:47,885] [INFO] Task started: fastANI
[2024-01-24 13:13:47,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg52e6d4af-aa11-4f6e-a456-e92171af8728/GCF_949281285.1_ASM94928128v1_genomic.fna.gz --refList GCF_949281285.1_ASM94928128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_949281285.1_ASM94928128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:56,797] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:56,810] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:56,810] [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_000964425.1	s__Komagataeibacter intermedius	99.8912	1093	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.80	99.80	0.96	0.96	2	conclusive
GCF_003207815.1	s__Komagataeibacter oboediens	94.4017	957	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.65	98.22	0.88	0.85	10	-
GCF_003207895.1	s__Komagataeibacter swingsii	89.7548	891	1213	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	89.6674	905	1213	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	89.3416	835	1213	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	88.948	891	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.62	98.62	0.92	0.92	2	-
GCF_009834365.1	s__Komagataeibacter xylinus_D	85.2807	856	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199155.1	s__Komagataeibacter kakiaceti	85.0185	776	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.94	99.94	1.00	1.00	2	-
GCF_003206495.1	s__Komagataeibacter entanii	81.8744	637	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.26	98.23	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:56,812] [INFO] GTDB search result was written to GCF_949281285.1_ASM94928128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:56,813] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:56,815] [INFO] DFAST_QC result json was written to GCF_949281285.1_ASM94928128v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:56,816] [INFO] DFAST_QC completed!
[2024-01-24 13:13:56,816] [INFO] Total running time: 0h1m18s