[2024-01-24 12:31:55,178] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:55,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:55,182] [INFO] DQC Reference Directory: /var/lib/cwl/stg35543847-46e9-4df7-9fa9-391a29721254/dqc_reference
[2024-01-24 12:31:56,405] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:56,406] [INFO] Task started: Prodigal
[2024-01-24 12:31:56,406] [INFO] Running command: gunzip -c /var/lib/cwl/stgd265ebb4-a401-4498-8f73-8941b7be167c/GCF_000963885.1_ASM96388v1_genomic.fna.gz | prodigal -d GCF_000963885.1_ASM96388v1_genomic.fna/cds.fna -a GCF_000963885.1_ASM96388v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:07,220] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:07,220] [INFO] Task started: HMMsearch
[2024-01-24 12:32:07,221] [INFO] Running command: hmmsearch --tblout GCF_000963885.1_ASM96388v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35543847-46e9-4df7-9fa9-391a29721254/dqc_reference/reference_markers.hmm GCF_000963885.1_ASM96388v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:07,522] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:07,523] [INFO] Found 6/6 markers.
[2024-01-24 12:32:07,558] [INFO] Query marker FASTA was written to GCF_000963885.1_ASM96388v1_genomic.fna/markers.fasta
[2024-01-24 12:32:07,559] [INFO] Task started: Blastn
[2024-01-24 12:32:07,559] [INFO] Running command: blastn -query GCF_000963885.1_ASM96388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35543847-46e9-4df7-9fa9-391a29721254/dqc_reference/reference_markers.fasta -out GCF_000963885.1_ASM96388v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:08,471] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:08,475] [INFO] Selected 23 target genomes.
[2024-01-24 12:32:08,476] [INFO] Target genome list was writen to GCF_000963885.1_ASM96388v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:08,491] [INFO] Task started: fastANI
[2024-01-24 12:32:08,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgd265ebb4-a401-4498-8f73-8941b7be167c/GCF_000963885.1_ASM96388v1_genomic.fna.gz --refList GCF_000963885.1_ASM96388v1_genomic.fna/target_genomes.txt --output GCF_000963885.1_ASM96388v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:23,974] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:23,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35543847-46e9-4df7-9fa9-391a29721254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:23,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35543847-46e9-4df7-9fa9-391a29721254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:23,993] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:23,993] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:23,993] [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
Tanticharoenia sakaeratensis	strain=NBRC 103193	GCA_000963885.1	444053	444053	type	True	100.0	1129	1131	95	conclusive
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_002005465.1	320497	320497	type	True	79.0025	291	1131	95	below_threshold
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_007991115.1	320497	320497	type	True	78.9981	285	1131	95	below_threshold
Acidomonas methanolica	strain=NBRC 104435	GCA_007988925.1	437	437	type	True	78.3644	278	1131	95	below_threshold
Acidomonas methanolica	strain=DSM 5432	GCA_004346035.1	437	437	type	True	78.35	283	1131	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	78.3085	265	1131	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	78.296	268	1131	95	below_threshold
Acidomonas methanolica	strain=MB58	GCA_000617865.1	437	437	type	True	78.2426	280	1131	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_001547995.1	91915	91915	suspected-type	True	78.0789	167	1131	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_007989265.1	91915	91915	suspected-type	True	78.047	165	1131	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	78.0048	278	1131	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	77.7481	265	1131	95	below_threshold
Komagataeibacter melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	77.6748	172	1131	95	below_threshold
Gluconobacter kanchanaburiensis	strain=NBRC 103587	GCA_007988905.1	563199	563199	type	True	77.5913	150	1131	95	below_threshold
Granulibacter bethesdensis	strain=CGDNIH1	GCA_000014285.2	364410	364410	type	True	77.0344	71	1131	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	76.4142	120	1131	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.4092	80	1131	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.2146	61	1131	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.2131	59	1131	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.9205	90	1131	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	75.7324	89	1131	95	below_threshold
Rhizobium freirei	strain=PRF 81	GCA_000359745.1	1353277	1353277	type	True	75.6039	61	1131	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.488	80	1131	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:23,995] [INFO] DFAST Taxonomy check result was written to GCF_000963885.1_ASM96388v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:23,996] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:23,996] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:23,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35543847-46e9-4df7-9fa9-391a29721254/dqc_reference/checkm_data
[2024-01-24 12:32:23,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:24,044] [INFO] Task started: CheckM
[2024-01-24 12:32:24,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000963885.1_ASM96388v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000963885.1_ASM96388v1_genomic.fna/checkm_input GCF_000963885.1_ASM96388v1_genomic.fna/checkm_result
[2024-01-24 12:33:01,228] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:01,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:01,254] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:01,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:01,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000963885.1_ASM96388v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:01,255] [INFO] Task started: Blastn
[2024-01-24 12:33:01,256] [INFO] Running command: blastn -query GCF_000963885.1_ASM96388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35543847-46e9-4df7-9fa9-391a29721254/dqc_reference/reference_markers_gtdb.fasta -out GCF_000963885.1_ASM96388v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:02,970] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:02,975] [INFO] Selected 19 target genomes.
[2024-01-24 12:33:02,975] [INFO] Target genome list was writen to GCF_000963885.1_ASM96388v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:02,989] [INFO] Task started: fastANI
[2024-01-24 12:33:02,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgd265ebb4-a401-4498-8f73-8941b7be167c/GCF_000963885.1_ASM96388v1_genomic.fna.gz --refList GCF_000963885.1_ASM96388v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000963885.1_ASM96388v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:15,251] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:15,270] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:15,271] [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_000963885.1	s__Tanticharoenia sakaeratensis	100.0	1129	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Tanticharoenia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002005465.1	s__Neoasaia chiangmaiensis	79.0025	291	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neoasaia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013376175.1	s__Ameyamaea chiangmaiensis	78.6011	210	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Ameyamaea	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004346035.1	s__Acidomonas methanolica	78.35	283	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
GCF_001547995.1	s__Asaia bogorensis	78.0862	166	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	-
GCF_018811945.1	s__Gluconobacter sp018811945	78.0299	221	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	78.0176	277	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_014174255.1	s__Gluconacetobacter sacchari	77.8948	262	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018256155.1	s__Gluconobacter sp018256155	77.8205	210	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174375.1	s__Gluconacetobacter asukensis	77.813	262	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	77.763	281	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350405.1	s__Gluconacetobacter liquefaciens	77.7375	264	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003403295.1	s__Komagataeibacter melaceti	77.6753	172	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	77.6037	260	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCF_014174215.1	s__Gluconacetobacter tumulicola	77.5034	272	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_005844085.1	s__Lichenicoccus roseus	77.2202	220	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014285.2	s__Granulibacter bethesdensis	77.0368	70	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Granulibacter	95.0	98.35	95.29	0.97	0.95	8	-
GCA_903881515.1	s__CAIRTN01 sp903881515	76.1607	105	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIRTN01	95.0	99.60	99.60	0.90	0.90	2	-
GCA_014376425.1	s__Rhodovarius sp014376425	75.8309	54	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:15,273] [INFO] GTDB search result was written to GCF_000963885.1_ASM96388v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:15,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:15,279] [INFO] DFAST_QC result json was written to GCF_000963885.1_ASM96388v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:15,280] [INFO] DFAST_QC completed!
[2024-01-24 12:33:15,280] [INFO] Total running time: 0h1m20s