[2023-06-29 21:28:14,993] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:28:14,996] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:28:14,996] [INFO] DQC Reference Directory: /var/lib/cwl/stg7269198a-3860-493d-b8fc-a47a1295e49c/dqc_reference
[2023-06-29 21:28:16,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:28:16,266] [INFO] Task started: Prodigal
[2023-06-29 21:28:16,267] [INFO] Running command: gunzip -c /var/lib/cwl/stg98595159-378e-480d-9ad5-f1820a830513/GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna.gz | prodigal -d GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/cds.fna -a GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:28:32,081] [INFO] Task succeeded: Prodigal
[2023-06-29 21:28:32,081] [INFO] Task started: HMMsearch
[2023-06-29 21:28:32,081] [INFO] Running command: hmmsearch --tblout GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7269198a-3860-493d-b8fc-a47a1295e49c/dqc_reference/reference_markers.hmm GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:28:32,426] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:28:32,427] [INFO] Found 6/6 markers.
[2023-06-29 21:28:32,488] [INFO] Query marker FASTA was written to GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/markers.fasta
[2023-06-29 21:28:32,489] [INFO] Task started: Blastn
[2023-06-29 21:28:32,489] [INFO] Running command: blastn -query GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/markers.fasta -db /var/lib/cwl/stg7269198a-3860-493d-b8fc-a47a1295e49c/dqc_reference/reference_markers.fasta -out GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:28:33,607] [INFO] Task succeeded: Blastn
[2023-06-29 21:28:33,613] [INFO] Selected 21 target genomes.
[2023-06-29 21:28:33,613] [INFO] Target genome list was writen to GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/target_genomes.txt
[2023-06-29 21:28:33,615] [INFO] Task started: fastANI
[2023-06-29 21:28:33,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg98595159-378e-480d-9ad5-f1820a830513/GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna.gz --refList GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/target_genomes.txt --output GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:28:53,882] [INFO] Task succeeded: fastANI
[2023-06-29 21:28:53,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7269198a-3860-493d-b8fc-a47a1295e49c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:28:53,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7269198a-3860-493d-b8fc-a47a1295e49c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:28:53,902] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:28:53,902] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:28:53,902] [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
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	81.3516	717	1660	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	81.2986	744	1660	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	80.9878	779	1660	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	80.9277	776	1660	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.2639	630	1660	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.2036	628	1660	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.1707	639	1660	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	79.9752	593	1660	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.934	612	1660	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.9167	618	1660	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.8545	599	1660	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.8226	774	1660	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	79.8224	645	1660	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	79.7481	633	1660	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.7209	729	1660	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.6873	579	1660	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	79.6701	672	1660	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.62	649	1660	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.5544	642	1660	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.5024	632	1660	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.184	622	1660	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:28:53,909] [INFO] DFAST Taxonomy check result was written to GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/tc_result.tsv
[2023-06-29 21:28:53,910] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:28:53,910] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:28:53,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7269198a-3860-493d-b8fc-a47a1295e49c/dqc_reference/checkm_data
[2023-06-29 21:28:53,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:28:53,999] [INFO] Task started: CheckM
[2023-06-29 21:28:53,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/checkm_input GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/checkm_result
[2023-06-29 21:30:25,706] [INFO] Task succeeded: CheckM
[2023-06-29 21:30:25,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 21:30:25,733] [INFO] ===== Completeness check finished =====
[2023-06-29 21:30:25,733] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:30:25,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/markers.fasta)
[2023-06-29 21:30:25,735] [INFO] Task started: Blastn
[2023-06-29 21:30:25,735] [INFO] Running command: blastn -query GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/markers.fasta -db /var/lib/cwl/stg7269198a-3860-493d-b8fc-a47a1295e49c/dqc_reference/reference_markers_gtdb.fasta -out GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:30:27,970] [INFO] Task succeeded: Blastn
[2023-06-29 21:30:27,974] [INFO] Selected 23 target genomes.
[2023-06-29 21:30:27,974] [INFO] Target genome list was writen to GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:30:28,009] [INFO] Task started: fastANI
[2023-06-29 21:30:28,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg98595159-378e-480d-9ad5-f1820a830513/GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna.gz --refList GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/target_genomes_gtdb.txt --output GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:30:53,370] [INFO] Task succeeded: fastANI
[2023-06-29 21:30:53,395] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:30:53,396] [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_903938815.1	s__Rubrivivax sp903938815	99.9022	1596	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.66	99.41	0.96	0.94	10	conclusive
GCA_018780805.1	s__Rubrivivax sp018780805	83.7413	971	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016515.1	s__Rubrivivax albus	83.2921	986	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	81.3005	644	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725505.1	s__Rubrivivax sp001725505	81.1637	638	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198735.1	s__Aquabacterium_A sp002198735	81.0554	879	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340905.1	s__Rubrivivax gelatinosus	81.0198	774	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016191995.1	s__Rubrivivax sp016191995	80.8547	680	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904426505.1	s__Rubrivivax sp904426505	80.8424	764	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	80.8231	822	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017795745.1	s__Piscinibacter sp017795745	80.7565	822	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707445.1	s__Rubrivivax sp016707445	80.7286	725	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.23	99.17	0.94	0.91	3	-
GCA_011525985.1	s__Rubrivivax sp011525985	80.6002	374	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	80.5837	717	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425905.1	s__Methylibium sp001425905	80.3478	615	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476235.1	s__Schlegelella thermodepolymerans	80.1891	637	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCA_000244995.1	s__Aquabacterium_A sp000244995	80.0688	755	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702655.1	s__CAIKUF01 sp016702655	79.7768	668	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657635.1	s__Kinneretia sp015657635	79.4778	589	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790285.1	s__Pelomonas sp016790285	79.4018	624	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204525.1	s__Paucibacter_A oligotrophus	78.6119	498	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003208485.1	s__Acidovorax sp003208485	78.3822	557	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852425.1	s__Paucibacter_A sp003852425	78.1125	454	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:30:53,398] [INFO] GTDB search result was written to GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/result_gtdb.tsv
[2023-06-29 21:30:53,398] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:30:53,405] [INFO] DFAST_QC result json was written to GCA_903940985.1_freshwater_MAG_---_Loc080925-4m_bin-0609_genomic.fna/dqc_result.json
[2023-06-29 21:30:53,406] [INFO] DFAST_QC completed!
[2023-06-29 21:30:53,406] [INFO] Total running time: 0h2m38s