[2023-06-19 00:40:31,638] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:40:31,643] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:40:31,643] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f30bea9-2dee-4460-849a-27cfdb54b52b/dqc_reference
[2023-06-19 00:40:32,832] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:40:32,832] [INFO] Task started: Prodigal
[2023-06-19 00:40:32,833] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6abf724-1e2d-4cba-83bc-27a30fccb37b/GCA_018060255.1_ASM1806025v1_genomic.fna.gz | prodigal -d GCA_018060255.1_ASM1806025v1_genomic.fna/cds.fna -a GCA_018060255.1_ASM1806025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:40:40,274] [INFO] Task succeeded: Prodigal
[2023-06-19 00:40:40,275] [INFO] Task started: HMMsearch
[2023-06-19 00:40:40,275] [INFO] Running command: hmmsearch --tblout GCA_018060255.1_ASM1806025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f30bea9-2dee-4460-849a-27cfdb54b52b/dqc_reference/reference_markers.hmm GCA_018060255.1_ASM1806025v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:40:40,523] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:40:40,525] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd6abf724-1e2d-4cba-83bc-27a30fccb37b/GCA_018060255.1_ASM1806025v1_genomic.fna.gz]
[2023-06-19 00:40:40,558] [INFO] Query marker FASTA was written to GCA_018060255.1_ASM1806025v1_genomic.fna/markers.fasta
[2023-06-19 00:40:40,558] [INFO] Task started: Blastn
[2023-06-19 00:40:40,558] [INFO] Running command: blastn -query GCA_018060255.1_ASM1806025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f30bea9-2dee-4460-849a-27cfdb54b52b/dqc_reference/reference_markers.fasta -out GCA_018060255.1_ASM1806025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:40:41,585] [INFO] Task succeeded: Blastn
[2023-06-19 00:40:41,588] [INFO] Selected 31 target genomes.
[2023-06-19 00:40:41,589] [INFO] Target genome list was writen to GCA_018060255.1_ASM1806025v1_genomic.fna/target_genomes.txt
[2023-06-19 00:40:41,593] [INFO] Task started: fastANI
[2023-06-19 00:40:41,593] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6abf724-1e2d-4cba-83bc-27a30fccb37b/GCA_018060255.1_ASM1806025v1_genomic.fna.gz --refList GCA_018060255.1_ASM1806025v1_genomic.fna/target_genomes.txt --output GCA_018060255.1_ASM1806025v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:41:03,673] [INFO] Task succeeded: fastANI
[2023-06-19 00:41:03,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f30bea9-2dee-4460-849a-27cfdb54b52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:41:03,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f30bea9-2dee-4460-849a-27cfdb54b52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:41:03,696] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:41:03,697] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 00:41:03,697] [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
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	80.1104	368	772	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	80.0672	370	772	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	79.4733	321	772	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	79.3755	274	772	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	79.3258	335	772	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	79.3208	282	772	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	79.301	320	772	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	79.2277	284	772	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.0169	321	772	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	78.9854	297	772	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	78.9592	357	772	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	78.9451	302	772	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.9125	291	772	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.8482	346	772	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.6622	303	772	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	78.6311	303	772	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.6205	310	772	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	78.5674	297	772	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	78.5316	292	772	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	78.427	295	772	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.155	277	772	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	78.0745	283	772	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	77.9581	289	772	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	77.8451	283	772	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	77.7324	204	772	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.6913	269	772	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	76.6119	240	772	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.5882	251	772	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	76.5315	239	772	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	76.1873	169	772	95	below_threshold
Pseudomonas nicosulfuronedens	strain=LAM1902	GCA_005877905.1	2571105	2571105	type	True	76.1768	154	772	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 00:41:03,700] [INFO] DFAST Taxonomy check result was written to GCA_018060255.1_ASM1806025v1_genomic.fna/tc_result.tsv
[2023-06-19 00:41:03,700] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:41:03,700] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:41:03,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f30bea9-2dee-4460-849a-27cfdb54b52b/dqc_reference/checkm_data
[2023-06-19 00:41:03,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:41:03,735] [INFO] Task started: CheckM
[2023-06-19 00:41:03,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018060255.1_ASM1806025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018060255.1_ASM1806025v1_genomic.fna/checkm_input GCA_018060255.1_ASM1806025v1_genomic.fna/checkm_result
[2023-06-19 00:41:29,936] [INFO] Task succeeded: CheckM
[2023-06-19 00:41:29,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:41:29,970] [INFO] ===== Completeness check finished =====
[2023-06-19 00:41:29,970] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:41:29,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018060255.1_ASM1806025v1_genomic.fna/markers.fasta)
[2023-06-19 00:41:29,970] [INFO] Task started: Blastn
[2023-06-19 00:41:29,971] [INFO] Running command: blastn -query GCA_018060255.1_ASM1806025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f30bea9-2dee-4460-849a-27cfdb54b52b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018060255.1_ASM1806025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:41:32,078] [INFO] Task succeeded: Blastn
[2023-06-19 00:41:32,085] [INFO] Selected 16 target genomes.
[2023-06-19 00:41:32,085] [INFO] Target genome list was writen to GCA_018060255.1_ASM1806025v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:41:32,115] [INFO] Task started: fastANI
[2023-06-19 00:41:32,115] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6abf724-1e2d-4cba-83bc-27a30fccb37b/GCA_018060255.1_ASM1806025v1_genomic.fna.gz --refList GCA_018060255.1_ASM1806025v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018060255.1_ASM1806025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:41:42,156] [INFO] Task succeeded: fastANI
[2023-06-19 00:41:42,170] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:41:42,170] [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_017347485.1	s__Desulfobacillus denitrificans	98.5506	632	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	98.90	98.32	0.92	0.90	5	conclusive
GCA_003105015.1	s__Desulfobacillus sp003105015	88.0909	561	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	97.07	97.07	0.88	0.88	2	-
GCA_011526165.1	s__Desulfobacillus sp011526165	87.2702	494	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	98.84	98.84	0.79	0.79	2	-
GCA_008933825.1	s__Desulfobacillus sp008933825	87.1851	487	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	99.14	98.51	0.86	0.84	3	-
GCA_016868295.1	s__Desulfobacillus sp016868295	86.9	493	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214145.1	s__Desulfobacillus sp016214145	86.7086	554	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791205.1	s__Desulfobacillus sp016791205	86.1704	461	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339315.1	s__Desulfobacillus sp905339315	86.0322	369	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	97.66	96.66	0.91	0.89	3	-
GCA_016880375.1	s__Desulfobacillus sp016880375	85.4866	335	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703785.1	s__Desulfobacillus sp016703785	84.3501	552	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519045.1	s__Azonexus agitatus	81.0523	289	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.62	98.62	0.86	0.86	2	-
GCF_008711155.1	s__Azonexus sp008711155	79.9835	269	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.59	97.59	0.92	0.92	2	-
GCA_008933675.1	s__Azonexus sp008933675	79.2963	305	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469765.1	s__Azonexus hortensis	79.2012	285	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791065.1	s__Azonexus sp016791065	78.7203	223	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:41:42,176] [INFO] GTDB search result was written to GCA_018060255.1_ASM1806025v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:41:42,176] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:41:42,187] [INFO] DFAST_QC result json was written to GCA_018060255.1_ASM1806025v1_genomic.fna/dqc_result.json
[2023-06-19 00:41:42,187] [INFO] DFAST_QC completed!
[2023-06-19 00:41:42,187] [INFO] Total running time: 0h1m11s