[2024-01-24 12:23:49,389] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:49,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:49,392] [INFO] DQC Reference Directory: /var/lib/cwl/stga8209c11-ef77-4380-8bab-95e31d824a81/dqc_reference
[2024-01-24 12:23:50,694] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:50,695] [INFO] Task started: Prodigal
[2024-01-24 12:23:50,695] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fd2ca90-cb99-44fa-b667-735eb2ad5507/GCF_007991375.1_ASM799137v1_genomic.fna.gz | prodigal -d GCF_007991375.1_ASM799137v1_genomic.fna/cds.fna -a GCF_007991375.1_ASM799137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:02,316] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:02,316] [INFO] Task started: HMMsearch
[2024-01-24 12:24:02,317] [INFO] Running command: hmmsearch --tblout GCF_007991375.1_ASM799137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8209c11-ef77-4380-8bab-95e31d824a81/dqc_reference/reference_markers.hmm GCF_007991375.1_ASM799137v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:02,613] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:02,615] [INFO] Found 6/6 markers.
[2024-01-24 12:24:02,661] [INFO] Query marker FASTA was written to GCF_007991375.1_ASM799137v1_genomic.fna/markers.fasta
[2024-01-24 12:24:02,662] [INFO] Task started: Blastn
[2024-01-24 12:24:02,662] [INFO] Running command: blastn -query GCF_007991375.1_ASM799137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8209c11-ef77-4380-8bab-95e31d824a81/dqc_reference/reference_markers.fasta -out GCF_007991375.1_ASM799137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:03,474] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:03,478] [INFO] Selected 18 target genomes.
[2024-01-24 12:24:03,479] [INFO] Target genome list was writen to GCF_007991375.1_ASM799137v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:03,490] [INFO] Task started: fastANI
[2024-01-24 12:24:03,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd2ca90-cb99-44fa-b667-735eb2ad5507/GCF_007991375.1_ASM799137v1_genomic.fna.gz --refList GCF_007991375.1_ASM799137v1_genomic.fna/target_genomes.txt --output GCF_007991375.1_ASM799137v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:15,743] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:15,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8209c11-ef77-4380-8bab-95e31d824a81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:15,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8209c11-ef77-4380-8bab-95e31d824a81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:15,766] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:24:15,766] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:15,767] [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 nitrogenifigens	strain=NBRC 105050	GCA_007991375.1	285268	285268	type	True	100.0	1362	1365	95	conclusive
Acetobacter nitrogenifigens	strain=DSM 23921	GCA_000429165.1	285268	285268	type	True	99.9962	1365	1365	95	conclusive
Acetobacter sacchari	strain=TBRC 11175	GCA_017377715.1	2661687	2661687	type	True	92.8325	1191	1365	95	below_threshold
Acetobacter aceti	strain=DSM 3508	GCA_004341595.1	435	435	type	True	78.6717	250	1365	95	below_threshold
Acetobacter aceti	strain=NBRC 14818	GCA_000193495.2	435	435	type	True	78.585	251	1365	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	78.4212	250	1365	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	78.3968	252	1365	95	below_threshold
Acetobacter fallax	strain=LMG 1636	GCA_011516735.1	1737473	1737473	type	True	78.3545	240	1365	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	78.023	259	1365	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	78.0199	250	1365	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.9846	132	1365	95	below_threshold
Komagataeibacter xylinus	strain=LMG 1515	GCA_003207915.1	28448	28448	suspected-type	True	77.7738	180	1365	95	below_threshold
Komagataeibacter xylinus	strain=NBRC 15237	GCA_001571345.1	28448	28448	suspected-type	True	77.7511	182	1365	95	below_threshold
Komagataeibacter melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	77.7496	191	1365	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	77.0783	86	1365	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.6723	150	1365	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.6399	82	1365	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.605	83	1365	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:15,768] [INFO] DFAST Taxonomy check result was written to GCF_007991375.1_ASM799137v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:15,769] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:15,769] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:15,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8209c11-ef77-4380-8bab-95e31d824a81/dqc_reference/checkm_data
[2024-01-24 12:24:15,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:15,821] [INFO] Task started: CheckM
[2024-01-24 12:24:15,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991375.1_ASM799137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991375.1_ASM799137v1_genomic.fna/checkm_input GCF_007991375.1_ASM799137v1_genomic.fna/checkm_result
[2024-01-24 12:24:52,996] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:52,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:53,018] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:53,018] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:53,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991375.1_ASM799137v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:53,019] [INFO] Task started: Blastn
[2024-01-24 12:24:53,019] [INFO] Running command: blastn -query GCF_007991375.1_ASM799137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8209c11-ef77-4380-8bab-95e31d824a81/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991375.1_ASM799137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:54,499] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:54,506] [INFO] Selected 16 target genomes.
[2024-01-24 12:24:54,507] [INFO] Target genome list was writen to GCF_007991375.1_ASM799137v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:54,517] [INFO] Task started: fastANI
[2024-01-24 12:24:54,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd2ca90-cb99-44fa-b667-735eb2ad5507/GCF_007991375.1_ASM799137v1_genomic.fna.gz --refList GCF_007991375.1_ASM799137v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991375.1_ASM799137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:05,006] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:05,019] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:05,019] [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_000429165.1	s__Acetobacter nitrogenifigens	99.9962	1365	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017377715.1	s__Acetobacter sacchari	92.8191	1192	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002153745.1	s__Acetobacter sp002153745	91.9374	787	1365	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	78.6278	250	1365	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	78.585	251	1365	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	78.5629	233	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516765.1	s__Acetobacter sicerae	78.5162	278	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	78.3898	252	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_011516735.1	s__Acetobacter fallax	78.3545	240	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013376175.1	s__Ameyamaea chiangmaiensis	78.2112	200	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Ameyamaea	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003350405.1	s__Gluconacetobacter liquefaciens	78.0664	254	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002409645.1	s__Acetobacter sp002409645	77.8752	227	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	77.832	277	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403295.1	s__Komagataeibacter melaceti	77.7663	190	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571345.1	s__Komagataeibacter xylinus	77.7511	182	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.56	99.15	0.93	0.88	3	-
GCF_004302915.1	s__Komagataeibacter xylinus_C	77.7273	194	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:05,021] [INFO] GTDB search result was written to GCF_007991375.1_ASM799137v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:05,022] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:05,029] [INFO] DFAST_QC result json was written to GCF_007991375.1_ASM799137v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:05,029] [INFO] DFAST_QC completed!
[2024-01-24 12:25:05,029] [INFO] Total running time: 0h1m16s