[2024-01-24 13:49:25,566] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:25,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:25,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bbecdb8-0fec-4b8a-a03e-76c8ffd17175/dqc_reference
[2024-01-24 13:49:26,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:26,955] [INFO] Task started: Prodigal
[2024-01-24 13:49:26,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8d7ffba-44df-4e54-b9de-4d1325ffc57c/GCF_000014285.2_ASM1428v2_genomic.fna.gz | prodigal -d GCF_000014285.2_ASM1428v2_genomic.fna/cds.fna -a GCF_000014285.2_ASM1428v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:36,274] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:36,275] [INFO] Task started: HMMsearch
[2024-01-24 13:49:36,275] [INFO] Running command: hmmsearch --tblout GCF_000014285.2_ASM1428v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bbecdb8-0fec-4b8a-a03e-76c8ffd17175/dqc_reference/reference_markers.hmm GCF_000014285.2_ASM1428v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:36,536] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:36,538] [INFO] Found 6/6 markers.
[2024-01-24 13:49:36,567] [INFO] Query marker FASTA was written to GCF_000014285.2_ASM1428v2_genomic.fna/markers.fasta
[2024-01-24 13:49:36,568] [INFO] Task started: Blastn
[2024-01-24 13:49:36,568] [INFO] Running command: blastn -query GCF_000014285.2_ASM1428v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bbecdb8-0fec-4b8a-a03e-76c8ffd17175/dqc_reference/reference_markers.fasta -out GCF_000014285.2_ASM1428v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:37,339] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:37,343] [INFO] Selected 26 target genomes.
[2024-01-24 13:49:37,343] [INFO] Target genome list was writen to GCF_000014285.2_ASM1428v2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:37,362] [INFO] Task started: fastANI
[2024-01-24 13:49:37,362] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8d7ffba-44df-4e54-b9de-4d1325ffc57c/GCF_000014285.2_ASM1428v2_genomic.fna.gz --refList GCF_000014285.2_ASM1428v2_genomic.fna/target_genomes.txt --output GCF_000014285.2_ASM1428v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:55,279] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:55,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bbecdb8-0fec-4b8a-a03e-76c8ffd17175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:55,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bbecdb8-0fec-4b8a-a03e-76c8ffd17175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:55,297] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:55,297] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:55,297] [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
Granulibacter bethesdensis	strain=CGDNIH1	GCA_000014285.2	364410	364410	type	True	100.0	901	902	95	conclusive
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	78.0635	119	902	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	77.9075	124	902	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.6789	141	902	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	77.5651	113	902	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.2706	102	902	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	77.2502	122	902	95	below_threshold
Acidocella facilis	strain=ATCC 35904	GCA_000687875.1	525	525	type	True	77.2154	126	902	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	77.1037	92	902	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	77.0266	110	902	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	77.0138	92	902	95	below_threshold
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	76.985	88	902	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	76.9511	98	902	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	76.8759	91	902	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	76.8266	114	902	95	below_threshold
Tanticharoenia sakaeratensis	strain=NBRC 103193	GCA_000963885.1	444053	444053	type	True	76.739	78	902	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.6913	96	902	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	76.6159	111	902	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	76.5858	97	902	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	76.5503	117	902	95	below_threshold
Roseomonas vastitatis	strain=CPCC 101021	GCA_003604215.1	2307076	2307076	type	True	76.431	101	902	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	76.3576	106	902	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:55,299] [INFO] DFAST Taxonomy check result was written to GCF_000014285.2_ASM1428v2_genomic.fna/tc_result.tsv
[2024-01-24 13:49:55,300] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:55,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:55,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bbecdb8-0fec-4b8a-a03e-76c8ffd17175/dqc_reference/checkm_data
[2024-01-24 13:49:55,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:55,337] [INFO] Task started: CheckM
[2024-01-24 13:49:55,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000014285.2_ASM1428v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000014285.2_ASM1428v2_genomic.fna/checkm_input GCF_000014285.2_ASM1428v2_genomic.fna/checkm_result
[2024-01-24 13:50:27,027] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:27,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:27,045] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:27,045] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:27,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000014285.2_ASM1428v2_genomic.fna/markers.fasta)
[2024-01-24 13:50:27,046] [INFO] Task started: Blastn
[2024-01-24 13:50:27,046] [INFO] Running command: blastn -query GCF_000014285.2_ASM1428v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bbecdb8-0fec-4b8a-a03e-76c8ffd17175/dqc_reference/reference_markers_gtdb.fasta -out GCF_000014285.2_ASM1428v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:28,292] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:28,296] [INFO] Selected 19 target genomes.
[2024-01-24 13:50:28,297] [INFO] Target genome list was writen to GCF_000014285.2_ASM1428v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:28,778] [INFO] Task started: fastANI
[2024-01-24 13:50:28,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8d7ffba-44df-4e54-b9de-4d1325ffc57c/GCF_000014285.2_ASM1428v2_genomic.fna.gz --refList GCF_000014285.2_ASM1428v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000014285.2_ASM1428v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:42,591] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:42,607] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:42,608] [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_000014285.2	s__Granulibacter bethesdensis	100.0	901	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Granulibacter	95.0	98.35	95.29	0.97	0.95	8	conclusive
GCF_001889545.1	s__Granulibacter bethesdensis_B	92.1458	833	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Granulibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	78.0509	120	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_009834365.1	s__Komagataeibacter xylinus_D	77.9271	96	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174165.1	s__Gluconacetobacter dulcium	77.2502	122	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	-
GCA_018971455.1	s__REEB85 sp018971455	77.0651	86	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__REEB85	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765865.1	s__Acidisoma sp009765865	77.0377	106	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisoma	95.0	99.17	99.17	0.87	0.87	2	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	76.9889	119	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881515.1	s__CAIRTN01 sp903881515	76.9273	87	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIRTN01	95.0	99.60	99.60	0.90	0.90	2	-
GCF_014644535.1	s__Roseomonas_B lacus	76.8759	91	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899585.1	s__70-18 sp001899585	76.7937	166	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCF_003173615.1	s__Roseomonas_A sp003173615	76.7085	85	902	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_019024325.1	s__Roseomonas_A tokyonensis	76.5704	118	902	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_001982615.1	s__Roseomonas deserti	76.5647	98	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903864895.1	s__CAIPHQ01 sp903864895	76.5152	135	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIPHQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918195.1	s__BOG-930 sp903918195	76.4316	116	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCA_903844785.1	s__Roseomonas_B sp903844785	76.3518	57	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376425.1	s__Rhodovarius sp014376425	76.0964	59	902	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 13:50:42,609] [INFO] GTDB search result was written to GCF_000014285.2_ASM1428v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:42,610] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:42,615] [INFO] DFAST_QC result json was written to GCF_000014285.2_ASM1428v2_genomic.fna/dqc_result.json
[2024-01-24 13:50:42,615] [INFO] DFAST_QC completed!
[2024-01-24 13:50:42,615] [INFO] Total running time: 0h1m17s