[2023-06-08 16:39:11,150] [INFO] DFAST_QC pipeline started.
[2023-06-08 16:39:11,153] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 16:39:11,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f95af07-b197-447a-9d60-456bff74cbac/dqc_reference
[2023-06-08 16:39:12,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 16:39:12,347] [INFO] Task started: Prodigal
[2023-06-08 16:39:12,348] [INFO] Running command: gunzip -c /var/lib/cwl/stg19e613f1-1c9a-4d89-8b49-eadfd753c3b4/GCA_902826095.1_RBC008_genomic.fna.gz | prodigal -d GCA_902826095.1_RBC008_genomic.fna/cds.fna -a GCA_902826095.1_RBC008_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 16:39:22,162] [INFO] Task succeeded: Prodigal
[2023-06-08 16:39:22,162] [INFO] Task started: HMMsearch
[2023-06-08 16:39:22,163] [INFO] Running command: hmmsearch --tblout GCA_902826095.1_RBC008_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f95af07-b197-447a-9d60-456bff74cbac/dqc_reference/reference_markers.hmm GCA_902826095.1_RBC008_genomic.fna/protein.faa > /dev/null
[2023-06-08 16:39:22,411] [INFO] Task succeeded: HMMsearch
[2023-06-08 16:39:22,413] [INFO] Found 6/6 markers.
[2023-06-08 16:39:22,451] [INFO] Query marker FASTA was written to GCA_902826095.1_RBC008_genomic.fna/markers.fasta
[2023-06-08 16:39:22,451] [INFO] Task started: Blastn
[2023-06-08 16:39:22,452] [INFO] Running command: blastn -query GCA_902826095.1_RBC008_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f95af07-b197-447a-9d60-456bff74cbac/dqc_reference/reference_markers.fasta -out GCA_902826095.1_RBC008_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:39:23,373] [INFO] Task succeeded: Blastn
[2023-06-08 16:39:23,379] [INFO] Selected 22 target genomes.
[2023-06-08 16:39:23,380] [INFO] Target genome list was writen to GCA_902826095.1_RBC008_genomic.fna/target_genomes.txt
[2023-06-08 16:39:23,385] [INFO] Task started: fastANI
[2023-06-08 16:39:23,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e613f1-1c9a-4d89-8b49-eadfd753c3b4/GCA_902826095.1_RBC008_genomic.fna.gz --refList GCA_902826095.1_RBC008_genomic.fna/target_genomes.txt --output GCA_902826095.1_RBC008_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 16:39:37,897] [INFO] Task succeeded: fastANI
[2023-06-08 16:39:37,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f95af07-b197-447a-9d60-456bff74cbac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 16:39:37,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f95af07-b197-447a-9d60-456bff74cbac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 16:39:37,921] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 16:39:37,921] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 16:39:37,921] [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
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	77.3204	342	1236	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	77.3033	344	1236	95	below_threshold
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	77.2131	336	1236	95	below_threshold
Aquisalinus luteolus	strain=NH6-79	GCA_009712425.2	1566827	1566827	type	True	76.6947	103	1236	95	below_threshold
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	76.6524	105	1236	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	76.5624	131	1236	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	76.5461	132	1236	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	76.479	129	1236	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	76.3814	151	1236	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.3082	81	1236	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	76.0073	82	1236	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	76.0013	141	1236	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	75.9964	153	1236	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.9843	126	1236	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	75.9784	128	1236	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	75.96	128	1236	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	75.8559	151	1236	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	75.7029	104	1236	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.6342	106	1236	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.5561	158	1236	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.3848	193	1236	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.382	96	1236	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 16:39:37,923] [INFO] DFAST Taxonomy check result was written to GCA_902826095.1_RBC008_genomic.fna/tc_result.tsv
[2023-06-08 16:39:37,924] [INFO] ===== Taxonomy check completed =====
[2023-06-08 16:39:37,924] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 16:39:37,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f95af07-b197-447a-9d60-456bff74cbac/dqc_reference/checkm_data
[2023-06-08 16:39:37,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 16:39:37,968] [INFO] Task started: CheckM
[2023-06-08 16:39:37,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902826095.1_RBC008_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902826095.1_RBC008_genomic.fna/checkm_input GCA_902826095.1_RBC008_genomic.fna/checkm_result
[2023-06-08 16:40:10,467] [INFO] Task succeeded: CheckM
[2023-06-08 16:40:10,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 16:40:10,493] [INFO] ===== Completeness check finished =====
[2023-06-08 16:40:10,493] [INFO] ===== Start GTDB Search =====
[2023-06-08 16:40:10,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902826095.1_RBC008_genomic.fna/markers.fasta)
[2023-06-08 16:40:10,494] [INFO] Task started: Blastn
[2023-06-08 16:40:10,494] [INFO] Running command: blastn -query GCA_902826095.1_RBC008_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f95af07-b197-447a-9d60-456bff74cbac/dqc_reference/reference_markers_gtdb.fasta -out GCA_902826095.1_RBC008_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:40:12,182] [INFO] Task succeeded: Blastn
[2023-06-08 16:40:12,187] [INFO] Selected 16 target genomes.
[2023-06-08 16:40:12,187] [INFO] Target genome list was writen to GCA_902826095.1_RBC008_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 16:40:12,244] [INFO] Task started: fastANI
[2023-06-08 16:40:12,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e613f1-1c9a-4d89-8b49-eadfd753c3b4/GCA_902826095.1_RBC008_genomic.fna.gz --refList GCA_902826095.1_RBC008_genomic.fna/target_genomes_gtdb.txt --output GCA_902826095.1_RBC008_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 16:40:24,119] [INFO] Task succeeded: fastANI
[2023-06-08 16:40:24,137] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 16:40:24,138] [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_902826095.1	s__CV81 sp902826095	100.0	1235	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001767925.1	s__CV81 sp001767925	80.4649	580	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013389125.1	s__CV81 sp013389125	80.4169	510	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003506635.1	s__CV81 sp003506635	79.0335	419	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013389105.1	s__JACADZ01 sp013389105	77.4781	279	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__JACADZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	77.3106	343	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002943565.1	s__Marinicaulis flavus	77.2019	339	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125425.1	s__Amphiplicatus sp016125425	77.1919	289	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704915.1	s__Marinicaulis sp002704915	76.9121	248	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712425.2	s__Aquisalinus luteolus	76.6947	103	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001657385.1	s__Marinicaulis sp001657385	76.6416	276	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003015025.1	s__Nitratireductor_D sp003015025	75.9285	141	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCF_002088975.1	s__Henriciella aquimarina	75.7846	85	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765995.1	s__Roseiarcus sp009765995	75.5838	143	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Roseiarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019233695.1	s__JAFAME01 sp019233695	75.4637	88	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__JAFAME01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 16:40:24,140] [INFO] GTDB search result was written to GCA_902826095.1_RBC008_genomic.fna/result_gtdb.tsv
[2023-06-08 16:40:24,141] [INFO] ===== GTDB Search completed =====
[2023-06-08 16:40:24,145] [INFO] DFAST_QC result json was written to GCA_902826095.1_RBC008_genomic.fna/dqc_result.json
[2023-06-08 16:40:24,145] [INFO] DFAST_QC completed!
[2023-06-08 16:40:24,146] [INFO] Total running time: 0h1m13s