[2023-06-28 08:55:41,017] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:55:41,019] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:55:41,019] [INFO] DQC Reference Directory: /var/lib/cwl/stgb63b62b6-e2c4-43d2-894d-19aea16d1e4f/dqc_reference
[2023-06-28 08:55:42,327] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:55:42,328] [INFO] Task started: Prodigal
[2023-06-28 08:55:42,328] [INFO] Running command: gunzip -c /var/lib/cwl/stg83485404-688f-49a0-9e02-37683133b794/GCA_017302435.1_ASM1730243v1_genomic.fna.gz | prodigal -d GCA_017302435.1_ASM1730243v1_genomic.fna/cds.fna -a GCA_017302435.1_ASM1730243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:55:55,727] [INFO] Task succeeded: Prodigal
[2023-06-28 08:55:55,727] [INFO] Task started: HMMsearch
[2023-06-28 08:55:55,728] [INFO] Running command: hmmsearch --tblout GCA_017302435.1_ASM1730243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb63b62b6-e2c4-43d2-894d-19aea16d1e4f/dqc_reference/reference_markers.hmm GCA_017302435.1_ASM1730243v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:55:56,042] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:55:56,043] [INFO] Found 6/6 markers.
[2023-06-28 08:55:56,090] [INFO] Query marker FASTA was written to GCA_017302435.1_ASM1730243v1_genomic.fna/markers.fasta
[2023-06-28 08:55:56,091] [INFO] Task started: Blastn
[2023-06-28 08:55:56,091] [INFO] Running command: blastn -query GCA_017302435.1_ASM1730243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb63b62b6-e2c4-43d2-894d-19aea16d1e4f/dqc_reference/reference_markers.fasta -out GCA_017302435.1_ASM1730243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:55:57,114] [INFO] Task succeeded: Blastn
[2023-06-28 08:55:57,118] [INFO] Selected 20 target genomes.
[2023-06-28 08:55:57,118] [INFO] Target genome list was writen to GCA_017302435.1_ASM1730243v1_genomic.fna/target_genomes.txt
[2023-06-28 08:55:57,123] [INFO] Task started: fastANI
[2023-06-28 08:55:57,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg83485404-688f-49a0-9e02-37683133b794/GCA_017302435.1_ASM1730243v1_genomic.fna.gz --refList GCA_017302435.1_ASM1730243v1_genomic.fna/target_genomes.txt --output GCA_017302435.1_ASM1730243v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:56:14,442] [INFO] Task succeeded: fastANI
[2023-06-28 08:56:14,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb63b62b6-e2c4-43d2-894d-19aea16d1e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:56:14,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb63b62b6-e2c4-43d2-894d-19aea16d1e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:56:14,460] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:56:14,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 08:56:14,460] [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
Candidatus Accumulibacter contiguus		GCA_012940005.1	2954381	2954381	type	True	81.6239	799	1475	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	77.8726	334	1475	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	77.8512	332	1475	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.75	295	1475	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	77.5383	275	1475	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	77.3408	245	1475	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	77.3065	235	1475	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	77.2946	243	1475	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.2579	205	1475	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.1795	211	1475	95	below_threshold
Aromatoleum diolicum	strain=22Lin	GCA_012910955.1	75796	75796	type	True	76.8518	199	1475	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_012910925.1	76115	76115	type	True	76.8414	190	1475	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	76.7618	196	1475	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	76.6429	238	1475	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	76.3155	215	1475	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	76.2915	185	1475	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	75.8093	116	1475	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	75.805	128	1475	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	75.6493	116	1475	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	75.4598	80	1475	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 08:56:14,462] [INFO] DFAST Taxonomy check result was written to GCA_017302435.1_ASM1730243v1_genomic.fna/tc_result.tsv
[2023-06-28 08:56:14,462] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:56:14,463] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:56:14,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb63b62b6-e2c4-43d2-894d-19aea16d1e4f/dqc_reference/checkm_data
[2023-06-28 08:56:14,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:56:14,511] [INFO] Task started: CheckM
[2023-06-28 08:56:14,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017302435.1_ASM1730243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017302435.1_ASM1730243v1_genomic.fna/checkm_input GCA_017302435.1_ASM1730243v1_genomic.fna/checkm_result
[2023-06-28 08:56:56,607] [INFO] Task succeeded: CheckM
[2023-06-28 08:56:56,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:56:56,626] [INFO] ===== Completeness check finished =====
[2023-06-28 08:56:56,627] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:56:56,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017302435.1_ASM1730243v1_genomic.fna/markers.fasta)
[2023-06-28 08:56:56,627] [INFO] Task started: Blastn
[2023-06-28 08:56:56,628] [INFO] Running command: blastn -query GCA_017302435.1_ASM1730243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb63b62b6-e2c4-43d2-894d-19aea16d1e4f/dqc_reference/reference_markers_gtdb.fasta -out GCA_017302435.1_ASM1730243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:56:58,127] [INFO] Task succeeded: Blastn
[2023-06-28 08:56:58,131] [INFO] Selected 10 target genomes.
[2023-06-28 08:56:58,132] [INFO] Target genome list was writen to GCA_017302435.1_ASM1730243v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:56:58,133] [INFO] Task started: fastANI
[2023-06-28 08:56:58,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg83485404-688f-49a0-9e02-37683133b794/GCA_017302435.1_ASM1730243v1_genomic.fna.gz --refList GCA_017302435.1_ASM1730243v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017302435.1_ASM1730243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:57:08,268] [INFO] Task succeeded: fastANI
[2023-06-28 08:57:08,289] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:57:08,289] [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_017302435.1	s__Accumulibacter sp017302435	100.0	1468	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016709675.1	s__Accumulibacter sp016709675	91.5598	1144	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	98.87	98.87	0.92	0.92	2	-
GCA_016713625.1	s__Accumulibacter sp016713625	81.6946	833	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.10	99.10	0.76	0.76	2	-
GCF_012940005.1	s__Accumulibacter phosphatis_H	81.6354	798	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.13	99.13	0.91	0.91	2	-
GCA_016714935.1	s__Accumulibacter sp016714935	81.0061	699	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	98.82	98.60	0.85	0.81	4	-
GCF_000024165.1	s__Accumulibacter phosphatis_C	80.9319	790	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	98.52	96.04	0.92	0.86	4	-
GCA_002425405.1	s__Accumulibacter phosphatis_E	80.8336	687	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.65	99.65	0.90	0.90	2	-
GCF_005889575.1	s__Accumulibacter sp000584975	80.6718	720	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	98.95	98.61	0.89	0.84	7	-
GCF_900089955.1	s__Accumulibacter aalborgensis	80.6574	735	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789985.1	s__Accumulibacter sp016789985	80.1995	632	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:57:08,291] [INFO] GTDB search result was written to GCA_017302435.1_ASM1730243v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:57:08,292] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:57:08,296] [INFO] DFAST_QC result json was written to GCA_017302435.1_ASM1730243v1_genomic.fna/dqc_result.json
[2023-06-28 08:57:08,296] [INFO] DFAST_QC completed!
[2023-06-28 08:57:08,296] [INFO] Total running time: 0h1m27s