[2024-01-24 12:46:34,775] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:34,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:34,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fc3dc3a-7e38-4f32-b48a-c9fcebee591f/dqc_reference
[2024-01-24 12:46:35,922] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:35,922] [INFO] Task started: Prodigal
[2024-01-24 12:46:35,923] [INFO] Running command: gunzip -c /var/lib/cwl/stg94eaa64c-6ccb-42a8-8fce-ee2b7a9eaa85/GCF_002005465.1_ASM200546v1_genomic.fna.gz | prodigal -d GCF_002005465.1_ASM200546v1_genomic.fna/cds.fna -a GCF_002005465.1_ASM200546v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:46,175] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:46,176] [INFO] Task started: HMMsearch
[2024-01-24 12:46:46,176] [INFO] Running command: hmmsearch --tblout GCF_002005465.1_ASM200546v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fc3dc3a-7e38-4f32-b48a-c9fcebee591f/dqc_reference/reference_markers.hmm GCF_002005465.1_ASM200546v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:46,374] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:46,375] [INFO] Found 6/6 markers.
[2024-01-24 12:46:46,403] [INFO] Query marker FASTA was written to GCF_002005465.1_ASM200546v1_genomic.fna/markers.fasta
[2024-01-24 12:46:46,403] [INFO] Task started: Blastn
[2024-01-24 12:46:46,403] [INFO] Running command: blastn -query GCF_002005465.1_ASM200546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fc3dc3a-7e38-4f32-b48a-c9fcebee591f/dqc_reference/reference_markers.fasta -out GCF_002005465.1_ASM200546v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:47,150] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:47,153] [INFO] Selected 19 target genomes.
[2024-01-24 12:46:47,153] [INFO] Target genome list was writen to GCF_002005465.1_ASM200546v1_genomic.fna/target_genomes.txt
[2024-01-24 12:46:47,163] [INFO] Task started: fastANI
[2024-01-24 12:46:47,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg94eaa64c-6ccb-42a8-8fce-ee2b7a9eaa85/GCF_002005465.1_ASM200546v1_genomic.fna.gz --refList GCF_002005465.1_ASM200546v1_genomic.fna/target_genomes.txt --output GCF_002005465.1_ASM200546v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:58,151] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:58,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fc3dc3a-7e38-4f32-b48a-c9fcebee591f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:58,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fc3dc3a-7e38-4f32-b48a-c9fcebee591f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:58,165] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:46:58,166] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:58,166] [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
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_002005465.1	320497	320497	type	True	100.0	1134	1135	95	conclusive
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_007991115.1	320497	320497	type	True	99.993	1112	1135	95	conclusive
Tanticharoenia sakaeratensis	strain=NBRC 103193	GCA_000963885.1	444053	444053	type	True	79.2059	278	1135	95	below_threshold
Kozakia baliensis	strain=DSM 14400	GCA_001787335.1	153496	153496	type	True	78.9705	303	1135	95	below_threshold
Acidomonas methanolica	strain=DSM 5432	GCA_004346035.1	437	437	type	True	78.9339	368	1135	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	78.9277	281	1135	95	below_threshold
Acidomonas methanolica	strain=NBRC 104435	GCA_007988925.1	437	437	type	True	78.8819	368	1135	95	below_threshold
Acidomonas methanolica	strain=MB58	GCA_000617865.1	437	437	type	True	78.7697	347	1135	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	78.7605	263	1135	95	below_threshold
Kozakia baliensis	strain=NBRC 16664	GCA_007989365.1	153496	153496	type	True	78.5677	301	1135	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	78.3872	259	1135	95	below_threshold
Asaia prunellae	strain=JCM 25354	GCA_000613885.1	610245	610245	type	True	78.0232	161	1135	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	77.82	242	1135	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.6435	218	1135	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	76.5866	100	1135	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.4798	104	1135	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.2958	91	1135	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.187	90	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:58,168] [INFO] DFAST Taxonomy check result was written to GCF_002005465.1_ASM200546v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:58,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:58,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:58,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fc3dc3a-7e38-4f32-b48a-c9fcebee591f/dqc_reference/checkm_data
[2024-01-24 12:46:58,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:58,203] [INFO] Task started: CheckM
[2024-01-24 12:46:58,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002005465.1_ASM200546v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002005465.1_ASM200546v1_genomic.fna/checkm_input GCF_002005465.1_ASM200546v1_genomic.fna/checkm_result
[2024-01-24 12:47:33,939] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:33,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:33,962] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:33,963] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:33,963] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002005465.1_ASM200546v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:33,964] [INFO] Task started: Blastn
[2024-01-24 12:47:33,964] [INFO] Running command: blastn -query GCF_002005465.1_ASM200546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fc3dc3a-7e38-4f32-b48a-c9fcebee591f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002005465.1_ASM200546v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:35,256] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:35,259] [INFO] Selected 21 target genomes.
[2024-01-24 12:47:35,260] [INFO] Target genome list was writen to GCF_002005465.1_ASM200546v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:35,270] [INFO] Task started: fastANI
[2024-01-24 12:47:35,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg94eaa64c-6ccb-42a8-8fce-ee2b7a9eaa85/GCF_002005465.1_ASM200546v1_genomic.fna.gz --refList GCF_002005465.1_ASM200546v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002005465.1_ASM200546v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:48,147] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:48,164] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:48,164] [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_002005465.1	s__Neoasaia chiangmaiensis	100.0	1134	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neoasaia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000963885.1	s__Tanticharoenia sakaeratensis	79.1892	279	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Tanticharoenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001787335.1	s__Kozakia baliensis	78.9495	298	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Kozakia	95.0	98.19	97.27	0.93	0.89	4	-
GCF_004346035.1	s__Acidomonas methanolica	78.9346	368	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	78.7777	264	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_014635085.1	s__Asaia siamensis	78.3126	241	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018811945.1	s__Gluconobacter sp018811945	78.1208	234	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174305.1	s__Gluconacetobacter johannae	78.0626	237	1135	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	77.9686	219	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174155.1	s__Gluconacetobacter tumulisoli	77.9183	241	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988945.1	s__Swaminathania salitolerans	77.8584	258	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538885.1	s__Gluconobacter roseus	77.8363	210	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	77.8169	263	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCF_006539685.1	s__Gluconobacter oxydans	77.7025	203	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	-
GCF_009547075.1	s__Gluconobacter sp009547075	77.6427	218	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723915.1	s__Gluconobacter albidus	77.46	188	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_007988885.1	s__Gluconobacter_B wancherniae	77.1547	109	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_B	95.0	99.01	98.51	0.95	0.90	4	-
GCF_014490445.1	s__Roseomonas ludipueritiae	76.6815	105	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490485.1	s__Roseomonas aerophila	76.5866	100	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	76.2973	91	1135	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_017311575.1	s__Roseococcus thiosulfatophilus	76.187	90	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:48,166] [INFO] GTDB search result was written to GCF_002005465.1_ASM200546v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:48,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:48,171] [INFO] DFAST_QC result json was written to GCF_002005465.1_ASM200546v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:48,171] [INFO] DFAST_QC completed!
[2024-01-24 12:47:48,171] [INFO] Total running time: 0h1m13s