[2024-01-24 12:22:27,917] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:27,920] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:27,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg0726fa96-fd15-4fcf-ba47-d0405d092d4d/dqc_reference
[2024-01-24 12:22:29,460] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:29,461] [INFO] Task started: Prodigal
[2024-01-24 12:22:29,462] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bc66ceb-3d9f-402f-9800-9262d44438e1/GCF_009900765.1_ASM990076v1_genomic.fna.gz | prodigal -d GCF_009900765.1_ASM990076v1_genomic.fna/cds.fna -a GCF_009900765.1_ASM990076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:44,318] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:44,318] [INFO] Task started: HMMsearch
[2024-01-24 12:22:44,318] [INFO] Running command: hmmsearch --tblout GCF_009900765.1_ASM990076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0726fa96-fd15-4fcf-ba47-d0405d092d4d/dqc_reference/reference_markers.hmm GCF_009900765.1_ASM990076v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:44,633] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:44,634] [INFO] Found 6/6 markers.
[2024-01-24 12:22:44,675] [INFO] Query marker FASTA was written to GCF_009900765.1_ASM990076v1_genomic.fna/markers.fasta
[2024-01-24 12:22:44,675] [INFO] Task started: Blastn
[2024-01-24 12:22:44,675] [INFO] Running command: blastn -query GCF_009900765.1_ASM990076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0726fa96-fd15-4fcf-ba47-d0405d092d4d/dqc_reference/reference_markers.fasta -out GCF_009900765.1_ASM990076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:45,575] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:45,582] [INFO] Selected 17 target genomes.
[2024-01-24 12:22:45,582] [INFO] Target genome list was writen to GCF_009900765.1_ASM990076v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:45,593] [INFO] Task started: fastANI
[2024-01-24 12:22:45,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bc66ceb-3d9f-402f-9800-9262d44438e1/GCF_009900765.1_ASM990076v1_genomic.fna.gz --refList GCF_009900765.1_ASM990076v1_genomic.fna/target_genomes.txt --output GCF_009900765.1_ASM990076v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:04,813] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:04,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0726fa96-fd15-4fcf-ba47-d0405d092d4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:04,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0726fa96-fd15-4fcf-ba47-d0405d092d4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:04,829] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:04,830] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:04,830] [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
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	100.0	1473	1476	95	conclusive
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	87.5179	1205	1476	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	79.778	736	1476	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	79.5793	695	1476	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	79.2447	637	1476	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	79.0378	651	1476	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	78.9141	539	1476	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	78.8767	744	1476	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	78.8309	533	1476	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	78.7708	619	1476	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	78.7072	634	1476	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.7043	532	1476	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	78.6294	555	1476	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	78.481	627	1476	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.3529	604	1476	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	77.0356	260	1476	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	76.9709	271	1476	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:04,833] [INFO] DFAST Taxonomy check result was written to GCF_009900765.1_ASM990076v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:04,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:04,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:04,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0726fa96-fd15-4fcf-ba47-d0405d092d4d/dqc_reference/checkm_data
[2024-01-24 12:23:04,836] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:04,887] [INFO] Task started: CheckM
[2024-01-24 12:23:04,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009900765.1_ASM990076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009900765.1_ASM990076v1_genomic.fna/checkm_input GCF_009900765.1_ASM990076v1_genomic.fna/checkm_result
[2024-01-24 12:23:58,681] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:58,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:58,704] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:58,705] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:58,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009900765.1_ASM990076v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:58,706] [INFO] Task started: Blastn
[2024-01-24 12:23:58,706] [INFO] Running command: blastn -query GCF_009900765.1_ASM990076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0726fa96-fd15-4fcf-ba47-d0405d092d4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009900765.1_ASM990076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:00,379] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:00,382] [INFO] Selected 18 target genomes.
[2024-01-24 12:24:00,382] [INFO] Target genome list was writen to GCF_009900765.1_ASM990076v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:00,442] [INFO] Task started: fastANI
[2024-01-24 12:24:00,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bc66ceb-3d9f-402f-9800-9262d44438e1/GCF_009900765.1_ASM990076v1_genomic.fna.gz --refList GCF_009900765.1_ASM990076v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009900765.1_ASM990076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:19,887] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:19,914] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:19,915] [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_009900765.1	s__Rhodovarius lipocyclicus	100.0	1473	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004005855.1	s__Rhodovarius sp004005855	87.5336	1204	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129145.1	s__Roseococcus sp007129145	79.7828	333	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019083995.1	s__Roseococcus sp019083995	79.635	737	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017311575.1	s__Roseococcus thiosulfatophilus	79.5512	698	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425365.1	s__Roseococcus flocculans	79.348	671	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376425.1	s__Rhodovarius sp014376425	79.1165	552	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336745.1	s__Roseococcus sp004336745	79.1081	674	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018413645.1	s__Roseococcus sp018413645	79.0844	644	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298245.1	s__Rhodovarius sp013298245	79.0034	523	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490445.1	s__Roseomonas ludipueritiae	78.8416	545	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813355.1	s__Roseomonas_B sp017813355	78.8047	666	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	78.8041	615	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_016106015.1	s__Roseomonas_B sp016106015	78.6833	536	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011040385.1	s__Roseomonas_A sp011040385	78.4894	711	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622225.1	s__Roseomonas mucosa	78.4487	531	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.41	98.67	0.95	0.89	8	-
GCF_001941945.1	s__Roseomonas gilardii	78.3719	557	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	96.77	95.72	0.89	0.83	6	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	76.9887	270	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:19,916] [INFO] GTDB search result was written to GCF_009900765.1_ASM990076v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:19,917] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:19,921] [INFO] DFAST_QC result json was written to GCF_009900765.1_ASM990076v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:19,921] [INFO] DFAST_QC completed!
[2024-01-24 12:24:19,921] [INFO] Total running time: 0h1m52s