[2024-01-24 10:47:06,590] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgefa049af-0db0-4b02-9ec1-79f2f2ad7e7e/dqc_reference
[2024-01-24 10:47:12,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,810] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,811] [INFO] Running command: gunzip -c /var/lib/cwl/stgb661856e-4dc6-41a2-bf0f-8ef0e46d6fac/GCF_025995635.1_ASM2599563v1_genomic.fna.gz | prodigal -d GCF_025995635.1_ASM2599563v1_genomic.fna/cds.fna -a GCF_025995635.1_ASM2599563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:24,382] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:24,383] [INFO] Task started: HMMsearch
[2024-01-24 10:47:24,383] [INFO] Running command: hmmsearch --tblout GCF_025995635.1_ASM2599563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefa049af-0db0-4b02-9ec1-79f2f2ad7e7e/dqc_reference/reference_markers.hmm GCF_025995635.1_ASM2599563v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:24,724] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:24,725] [INFO] Found 6/6 markers.
[2024-01-24 10:47:24,762] [INFO] Query marker FASTA was written to GCF_025995635.1_ASM2599563v1_genomic.fna/markers.fasta
[2024-01-24 10:47:24,763] [INFO] Task started: Blastn
[2024-01-24 10:47:24,763] [INFO] Running command: blastn -query GCF_025995635.1_ASM2599563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefa049af-0db0-4b02-9ec1-79f2f2ad7e7e/dqc_reference/reference_markers.fasta -out GCF_025995635.1_ASM2599563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:25,517] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:25,522] [INFO] Selected 18 target genomes.
[2024-01-24 10:47:25,525] [INFO] Target genome list was writen to GCF_025995635.1_ASM2599563v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:26,032] [INFO] Task started: fastANI
[2024-01-24 10:47:26,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgb661856e-4dc6-41a2-bf0f-8ef0e46d6fac/GCF_025995635.1_ASM2599563v1_genomic.fna.gz --refList GCF_025995635.1_ASM2599563v1_genomic.fna/target_genomes.txt --output GCF_025995635.1_ASM2599563v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:39,451] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:39,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefa049af-0db0-4b02-9ec1-79f2f2ad7e7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:39,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefa049af-0db0-4b02-9ec1-79f2f2ad7e7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:39,468] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:39,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:39,468] [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=DSM 23921	GCA_000429165.1	285268	285268	type	True	99.9763	1349	1352	95	conclusive
Acetobacter nitrogenifigens	strain=NBRC 105050	GCA_007991375.1	285268	285268	type	True	99.9727	1315	1352	95	conclusive
Acetobacter sacchari	strain=TBRC 11175	GCA_017377715.1	2661687	2661687	type	True	92.8896	1168	1352	95	below_threshold
Acetobacter aceti	strain=DSM 3508	GCA_004341595.1	435	435	type	True	78.7296	247	1352	95	below_threshold
Acetobacter aceti	strain=NBRC 14818	GCA_000193495.2	435	435	type	True	78.7277	243	1352	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	78.4716	255	1352	95	below_threshold
Acetobacter fallax	strain=LMG 1636	GCA_011516735.1	1737473	1737473	type	True	78.4048	233	1352	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	78.3793	252	1352	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	78.2859	133	1352	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	78.0834	247	1352	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	78.0361	259	1352	95	below_threshold
Komagataeibacter xylinus	strain=LMG 1515	GCA_003207915.1	28448	28448	suspected-type	True	78.0014	183	1352	95	below_threshold
Komagataeibacter xylinus	strain=NBRC 15237	GCA_001571345.1	28448	28448	suspected-type	True	77.9998	176	1352	95	below_threshold
Komagataeibacter melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	77.7003	193	1352	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.9198	93	1352	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.6705	88	1352	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.6012	153	1352	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.4984	82	1352	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:39,489] [INFO] DFAST Taxonomy check result was written to GCF_025995635.1_ASM2599563v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:39,497] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:39,497] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:39,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefa049af-0db0-4b02-9ec1-79f2f2ad7e7e/dqc_reference/checkm_data
[2024-01-24 10:47:39,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:39,554] [INFO] Task started: CheckM
[2024-01-24 10:47:39,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995635.1_ASM2599563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995635.1_ASM2599563v1_genomic.fna/checkm_input GCF_025995635.1_ASM2599563v1_genomic.fna/checkm_result
[2024-01-24 10:48:17,832] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:17,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:17,858] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:17,859] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:17,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995635.1_ASM2599563v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:17,860] [INFO] Task started: Blastn
[2024-01-24 10:48:17,860] [INFO] Running command: blastn -query GCF_025995635.1_ASM2599563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefa049af-0db0-4b02-9ec1-79f2f2ad7e7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995635.1_ASM2599563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:19,055] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:19,064] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:19,064] [INFO] Target genome list was writen to GCF_025995635.1_ASM2599563v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:19,145] [INFO] Task started: fastANI
[2024-01-24 10:48:19,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgb661856e-4dc6-41a2-bf0f-8ef0e46d6fac/GCF_025995635.1_ASM2599563v1_genomic.fna.gz --refList GCF_025995635.1_ASM2599563v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995635.1_ASM2599563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:31,107] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:31,125] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:31,126] [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	99.9763	1349	1352	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	92.8896	1168	1352	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	91.8418	792	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005445.1	s__Acetobacter aceti_B	78.771	218	1352	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	78.7451	242	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.82	96.47	0.96	0.89	7	-
GCF_011516755.1	s__Acetobacter conturbans	78.5231	256	1352	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	78.4878	254	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_011516765.1	s__Acetobacter sicerae	78.4189	264	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516735.1	s__Acetobacter fallax	78.4048	233	1352	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	78.3267	197	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Ameyamaea	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002409645.1	s__Acetobacter sp002409645	78.0889	211	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350405.1	s__Gluconacetobacter liquefaciens	78.0687	255	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_019083805.1	s__Acetobacter estunensis_A	78.0333	236	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571345.1	s__Komagataeibacter xylinus	77.9998	176	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.56	99.15	0.93	0.88	3	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	77.9071	263	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004302915.1	s__Komagataeibacter xylinus_C	77.8899	193	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403295.1	s__Komagataeibacter melaceti	77.7003	193	1352	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 10:48:31,128] [INFO] GTDB search result was written to GCF_025995635.1_ASM2599563v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:31,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:31,132] [INFO] DFAST_QC result json was written to GCF_025995635.1_ASM2599563v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:31,132] [INFO] DFAST_QC completed!
[2024-01-24 10:48:31,132] [INFO] Total running time: 0h1m25s