[2023-06-18 10:25:43,871] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:25:43,873] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:25:43,874] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4856b7d-7814-47df-bfa0-d4fac4f58be9/dqc_reference
[2023-06-18 10:25:45,119] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:25:45,120] [INFO] Task started: Prodigal
[2023-06-18 10:25:45,120] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fcbe948-6722-40b0-bf59-acbb2e8274ee/GCA_018335835.1_ASM1833583v1_genomic.fna.gz | prodigal -d GCA_018335835.1_ASM1833583v1_genomic.fna/cds.fna -a GCA_018335835.1_ASM1833583v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:25:57,320] [INFO] Task succeeded: Prodigal
[2023-06-18 10:25:57,321] [INFO] Task started: HMMsearch
[2023-06-18 10:25:57,321] [INFO] Running command: hmmsearch --tblout GCA_018335835.1_ASM1833583v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4856b7d-7814-47df-bfa0-d4fac4f58be9/dqc_reference/reference_markers.hmm GCA_018335835.1_ASM1833583v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:25:57,612] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:25:57,616] [INFO] Found 6/6 markers.
[2023-06-18 10:25:57,668] [INFO] Query marker FASTA was written to GCA_018335835.1_ASM1833583v1_genomic.fna/markers.fasta
[2023-06-18 10:25:57,668] [INFO] Task started: Blastn
[2023-06-18 10:25:57,669] [INFO] Running command: blastn -query GCA_018335835.1_ASM1833583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4856b7d-7814-47df-bfa0-d4fac4f58be9/dqc_reference/reference_markers.fasta -out GCA_018335835.1_ASM1833583v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:25:58,643] [INFO] Task succeeded: Blastn
[2023-06-18 10:25:58,650] [INFO] Selected 12 target genomes.
[2023-06-18 10:25:58,651] [INFO] Target genome list was writen to GCA_018335835.1_ASM1833583v1_genomic.fna/target_genomes.txt
[2023-06-18 10:25:58,655] [INFO] Task started: fastANI
[2023-06-18 10:25:58,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fcbe948-6722-40b0-bf59-acbb2e8274ee/GCA_018335835.1_ASM1833583v1_genomic.fna.gz --refList GCA_018335835.1_ASM1833583v1_genomic.fna/target_genomes.txt --output GCA_018335835.1_ASM1833583v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:26:09,824] [INFO] Task succeeded: fastANI
[2023-06-18 10:26:09,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4856b7d-7814-47df-bfa0-d4fac4f58be9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:26:09,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4856b7d-7814-47df-bfa0-d4fac4f58be9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:26:09,839] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-06-18 10:26:09,839] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 10:26:09,839] [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
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	97.2373	940	1360	95	conclusive
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	86.9481	796	1360	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	82.0977	648	1360	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	82.086	646	1360	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	79.4212	366	1360	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.2666	398	1360	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	79.2353	410	1360	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.331	339	1360	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.0251	305	1360	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.4965	231	1360	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.3034	242	1360	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	77.0754	272	1360	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 10:26:09,843] [INFO] DFAST Taxonomy check result was written to GCA_018335835.1_ASM1833583v1_genomic.fna/tc_result.tsv
[2023-06-18 10:26:09,845] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:26:09,845] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:26:09,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4856b7d-7814-47df-bfa0-d4fac4f58be9/dqc_reference/checkm_data
[2023-06-18 10:26:09,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:26:09,897] [INFO] Task started: CheckM
[2023-06-18 10:26:09,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018335835.1_ASM1833583v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018335835.1_ASM1833583v1_genomic.fna/checkm_input GCA_018335835.1_ASM1833583v1_genomic.fna/checkm_result
[2023-06-18 10:26:48,996] [INFO] Task succeeded: CheckM
[2023-06-18 10:26:48,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 14.58%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-18 10:26:49,045] [INFO] ===== Completeness check finished =====
[2023-06-18 10:26:49,045] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:26:49,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018335835.1_ASM1833583v1_genomic.fna/markers.fasta)
[2023-06-18 10:26:49,046] [INFO] Task started: Blastn
[2023-06-18 10:26:49,046] [INFO] Running command: blastn -query GCA_018335835.1_ASM1833583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4856b7d-7814-47df-bfa0-d4fac4f58be9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018335835.1_ASM1833583v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:26:50,926] [INFO] Task succeeded: Blastn
[2023-06-18 10:26:50,933] [INFO] Selected 11 target genomes.
[2023-06-18 10:26:50,933] [INFO] Target genome list was writen to GCA_018335835.1_ASM1833583v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:26:50,939] [INFO] Task started: fastANI
[2023-06-18 10:26:50,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fcbe948-6722-40b0-bf59-acbb2e8274ee/GCA_018335835.1_ASM1833583v1_genomic.fna.gz --refList GCA_018335835.1_ASM1833583v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018335835.1_ASM1833583v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:27:00,215] [INFO] Task succeeded: fastANI
[2023-06-18 10:27:00,235] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:27:00,235] [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_000429605.1	s__Azonexus hydrophilus	97.2373	940	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.24	97.24	0.86	0.86	2	conclusive
GCA_002470165.1	s__Azonexus sp002470165	93.5762	592	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425245.1	s__Azonexus sp002425245	88.1233	685	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634965.1	s__Azonexus fungiphilus	86.9481	796	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.36	98.36	0.85	0.85	2	-
GCF_001956855.1	s__Azonexus hydrophilus_A	85.9329	819	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848965.1	s__Azonexus aromaticus_B	85.656	779	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933675.1	s__Azonexus sp008933675	83.7994	621	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008711155.1	s__Azonexus sp008711155	83.4053	644	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.59	97.59	0.92	0.92	2	-
GCA_002345845.1	s__Azonexus sp002345845	82.7512	631	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519045.1	s__Azonexus agitatus	82.5562	629	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.62	98.62	0.86	0.86	2	-
GCF_012275485.1	s__Azonexus sp012275485	81.3611	605	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 10:27:00,237] [INFO] GTDB search result was written to GCA_018335835.1_ASM1833583v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:27:00,240] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:27:00,244] [INFO] DFAST_QC result json was written to GCA_018335835.1_ASM1833583v1_genomic.fna/dqc_result.json
[2023-06-18 10:27:00,244] [INFO] DFAST_QC completed!
[2023-06-18 10:27:00,245] [INFO] Total running time: 0h1m16s