[2023-06-13 18:54:17,197] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:54:17,198] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:54:17,198] [INFO] DQC Reference Directory: /var/lib/cwl/stg94e9094c-1bfc-4c8f-ac38-2a6c3c59eced/dqc_reference
[2023-06-13 18:54:18,832] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:54:18,832] [INFO] Task started: Prodigal
[2023-06-13 18:54:18,832] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf2144e3-a3a1-4cc5-bd82-509fd52ad607/GCA_947459405.1_RE-18aug17-354_genomic.fna.gz | prodigal -d GCA_947459405.1_RE-18aug17-354_genomic.fna/cds.fna -a GCA_947459405.1_RE-18aug17-354_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:54:26,260] [INFO] Task succeeded: Prodigal
[2023-06-13 18:54:26,260] [INFO] Task started: HMMsearch
[2023-06-13 18:54:26,260] [INFO] Running command: hmmsearch --tblout GCA_947459405.1_RE-18aug17-354_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94e9094c-1bfc-4c8f-ac38-2a6c3c59eced/dqc_reference/reference_markers.hmm GCA_947459405.1_RE-18aug17-354_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:54:26,436] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:54:26,437] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcf2144e3-a3a1-4cc5-bd82-509fd52ad607/GCA_947459405.1_RE-18aug17-354_genomic.fna.gz]
[2023-06-13 18:54:26,465] [INFO] Query marker FASTA was written to GCA_947459405.1_RE-18aug17-354_genomic.fna/markers.fasta
[2023-06-13 18:54:26,465] [INFO] Task started: Blastn
[2023-06-13 18:54:26,465] [INFO] Running command: blastn -query GCA_947459405.1_RE-18aug17-354_genomic.fna/markers.fasta -db /var/lib/cwl/stg94e9094c-1bfc-4c8f-ac38-2a6c3c59eced/dqc_reference/reference_markers.fasta -out GCA_947459405.1_RE-18aug17-354_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:54:27,137] [INFO] Task succeeded: Blastn
[2023-06-13 18:54:27,141] [INFO] Selected 21 target genomes.
[2023-06-13 18:54:27,141] [INFO] Target genome list was writen to GCA_947459405.1_RE-18aug17-354_genomic.fna/target_genomes.txt
[2023-06-13 18:54:27,151] [INFO] Task started: fastANI
[2023-06-13 18:54:27,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf2144e3-a3a1-4cc5-bd82-509fd52ad607/GCA_947459405.1_RE-18aug17-354_genomic.fna.gz --refList GCA_947459405.1_RE-18aug17-354_genomic.fna/target_genomes.txt --output GCA_947459405.1_RE-18aug17-354_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:54:44,250] [INFO] Task succeeded: fastANI
[2023-06-13 18:54:44,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94e9094c-1bfc-4c8f-ac38-2a6c3c59eced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:54:44,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94e9094c-1bfc-4c8f-ac38-2a6c3c59eced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:54:44,263] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:54:44,263] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 18:54:44,264] [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
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.1395	383	808	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	79.1081	370	808	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	78.9329	341	808	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	78.9242	358	808	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	78.914	330	808	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.903	358	808	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	78.8873	327	808	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	78.83	339	808	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	78.8213	340	808	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	78.6614	326	808	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	78.6069	287	808	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	78.563	321	808	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	78.5563	265	808	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	78.5123	285	808	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	78.4709	323	808	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	78.402	357	808	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	78.3302	248	808	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	78.2999	310	808	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	78.2675	255	808	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	78.2359	270	808	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	77.9603	316	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 18:54:44,268] [INFO] DFAST Taxonomy check result was written to GCA_947459405.1_RE-18aug17-354_genomic.fna/tc_result.tsv
[2023-06-13 18:54:44,269] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:54:44,269] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:54:44,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94e9094c-1bfc-4c8f-ac38-2a6c3c59eced/dqc_reference/checkm_data
[2023-06-13 18:54:44,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:54:44,301] [INFO] Task started: CheckM
[2023-06-13 18:54:44,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947459405.1_RE-18aug17-354_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947459405.1_RE-18aug17-354_genomic.fna/checkm_input GCA_947459405.1_RE-18aug17-354_genomic.fna/checkm_result
[2023-06-13 18:55:10,803] [INFO] Task succeeded: CheckM
[2023-06-13 18:55:10,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.00%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:55:10,826] [INFO] ===== Completeness check finished =====
[2023-06-13 18:55:10,826] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:55:10,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947459405.1_RE-18aug17-354_genomic.fna/markers.fasta)
[2023-06-13 18:55:10,827] [INFO] Task started: Blastn
[2023-06-13 18:55:10,827] [INFO] Running command: blastn -query GCA_947459405.1_RE-18aug17-354_genomic.fna/markers.fasta -db /var/lib/cwl/stg94e9094c-1bfc-4c8f-ac38-2a6c3c59eced/dqc_reference/reference_markers_gtdb.fasta -out GCA_947459405.1_RE-18aug17-354_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:55:12,044] [INFO] Task succeeded: Blastn
[2023-06-13 18:55:12,051] [INFO] Selected 21 target genomes.
[2023-06-13 18:55:12,051] [INFO] Target genome list was writen to GCA_947459405.1_RE-18aug17-354_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:55:12,103] [INFO] Task started: fastANI
[2023-06-13 18:55:12,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf2144e3-a3a1-4cc5-bd82-509fd52ad607/GCA_947459405.1_RE-18aug17-354_genomic.fna.gz --refList GCA_947459405.1_RE-18aug17-354_genomic.fna/target_genomes_gtdb.txt --output GCA_947459405.1_RE-18aug17-354_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:55:28,642] [INFO] Task succeeded: fastANI
[2023-06-13 18:55:28,655] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 18:55:28,656] [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
GCA_005503335.1	s__SCMQ01 sp005503335	79.5459	380	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	79.5366	340	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868205.1	s__Polaromonas sp016868205	79.4882	397	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103405.1	s__Polaromonas sp900103405	79.2526	363	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282655.1	s__Polaromonas sp000282655	79.1378	360	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823485.1	s__Hydrogenophaga sp013823485	79.0727	297	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	98.29	98.29	0.80	0.80	2	-
GCA_013693755.1	s__Tibeticola sp013693755	78.9902	326	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCF_000745855.1	s__Xenophilus azovorans	78.9617	348	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xenophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652235.1	s__Pseudorhodoferax aquiterrae	78.9599	339	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476815.1	s__Pseudacidovorax intermedius_A	78.934	327	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778345.1	s__Ramlibacter sp013778345	78.903	358	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003711205.1	s__Polaromonas sp003711205	78.8549	342	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001580455.1	s__Ramlibacter tataouinensis_B	78.7885	324	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053545.1	s__Acidovorax sp003053545	78.6636	358	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCA_018241225.1	s__Variovorax sp018241225	78.5823	346	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002705.1	s__Rhodoferax_A sp002002705	78.5535	322	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241405.1	s__Alicycliphilus sp018241405	78.5444	277	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	98.75	98.75	0.95	0.95	2	-
GCF_013087525.1	s__Ramlibacter sp013087525	78.5024	338	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824015.1	s__Polaromonas sp013824015	78.4991	320	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556705.1	s__Tepidimonas thermarum	78.3452	247	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556605.1	s__Tepidimonas sediminis	78.2217	271	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 18:55:28,658] [INFO] GTDB search result was written to GCA_947459405.1_RE-18aug17-354_genomic.fna/result_gtdb.tsv
[2023-06-13 18:55:28,658] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:55:28,662] [INFO] DFAST_QC result json was written to GCA_947459405.1_RE-18aug17-354_genomic.fna/dqc_result.json
[2023-06-13 18:55:28,662] [INFO] DFAST_QC completed!
[2023-06-13 18:55:28,662] [INFO] Total running time: 0h1m11s