[2023-06-29 12:49:24,962] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:49:24,964] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:49:24,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bf2c90e-5cb0-480a-a15b-2b53f9ccde4e/dqc_reference
[2023-06-29 12:49:26,187] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:49:26,188] [INFO] Task started: Prodigal
[2023-06-29 12:49:26,188] [INFO] Running command: gunzip -c /var/lib/cwl/stgd65622e3-ae4b-4ce1-a306-7495274ba95d/GCA_021783525.1_ASM2178352v1_genomic.fna.gz | prodigal -d GCA_021783525.1_ASM2178352v1_genomic.fna/cds.fna -a GCA_021783525.1_ASM2178352v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:49:31,526] [INFO] Task succeeded: Prodigal
[2023-06-29 12:49:31,527] [INFO] Task started: HMMsearch
[2023-06-29 12:49:31,527] [INFO] Running command: hmmsearch --tblout GCA_021783525.1_ASM2178352v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bf2c90e-5cb0-480a-a15b-2b53f9ccde4e/dqc_reference/reference_markers.hmm GCA_021783525.1_ASM2178352v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:49:31,728] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:49:31,729] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd65622e3-ae4b-4ce1-a306-7495274ba95d/GCA_021783525.1_ASM2178352v1_genomic.fna.gz]
[2023-06-29 12:49:31,810] [INFO] Query marker FASTA was written to GCA_021783525.1_ASM2178352v1_genomic.fna/markers.fasta
[2023-06-29 12:49:31,811] [INFO] Task started: Blastn
[2023-06-29 12:49:31,811] [INFO] Running command: blastn -query GCA_021783525.1_ASM2178352v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bf2c90e-5cb0-480a-a15b-2b53f9ccde4e/dqc_reference/reference_markers.fasta -out GCA_021783525.1_ASM2178352v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:49:32,553] [INFO] Task succeeded: Blastn
[2023-06-29 12:49:32,557] [INFO] Selected 19 target genomes.
[2023-06-29 12:49:32,558] [INFO] Target genome list was writen to GCA_021783525.1_ASM2178352v1_genomic.fna/target_genomes.txt
[2023-06-29 12:49:32,562] [INFO] Task started: fastANI
[2023-06-29 12:49:32,562] [INFO] Running command: fastANI --query /var/lib/cwl/stgd65622e3-ae4b-4ce1-a306-7495274ba95d/GCA_021783525.1_ASM2178352v1_genomic.fna.gz --refList GCA_021783525.1_ASM2178352v1_genomic.fna/target_genomes.txt --output GCA_021783525.1_ASM2178352v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:49:42,631] [INFO] Task succeeded: fastANI
[2023-06-29 12:49:42,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bf2c90e-5cb0-480a-a15b-2b53f9ccde4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:49:42,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bf2c90e-5cb0-480a-a15b-2b53f9ccde4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:49:42,648] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:49:42,648] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:49:42,649] [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
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	79.3164	210	518	95	below_threshold
Ferriphaselus amnicola	strain=OYT1	GCA_000974685.2	1188319	1188319	type	True	77.5867	123	518	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.1035	104	518	95	below_threshold
Gallionella capsiferriformans	strain=ES-2	GCA_000145255.1	370405	370405	type	True	77.0316	67	518	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.9492	78	518	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	76.9149	72	518	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.8337	87	518	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	76.7854	87	518	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	76.6886	105	518	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	76.6535	68	518	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	76.6414	75	518	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	76.4609	66	518	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	76.4587	55	518	95	below_threshold
Ralstonia solanacearum	strain=NCPPB 325	GCA_015910705.1	305	305	type	True	76.3339	82	518	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	76.3107	90	518	95	below_threshold
Ralstonia solanacearum	strain=K60	GCA_002251695.1	305	305	type	True	76.2663	80	518	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	76.2535	59	518	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:49:42,651] [INFO] DFAST Taxonomy check result was written to GCA_021783525.1_ASM2178352v1_genomic.fna/tc_result.tsv
[2023-06-29 12:49:42,651] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:49:42,651] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:49:42,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bf2c90e-5cb0-480a-a15b-2b53f9ccde4e/dqc_reference/checkm_data
[2023-06-29 12:49:42,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:49:42,680] [INFO] Task started: CheckM
[2023-06-29 12:49:42,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021783525.1_ASM2178352v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021783525.1_ASM2178352v1_genomic.fna/checkm_input GCA_021783525.1_ASM2178352v1_genomic.fna/checkm_result
[2023-06-29 12:50:04,650] [INFO] Task succeeded: CheckM
[2023-06-29 12:50:04,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:50:04,673] [INFO] ===== Completeness check finished =====
[2023-06-29 12:50:04,673] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:50:04,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021783525.1_ASM2178352v1_genomic.fna/markers.fasta)
[2023-06-29 12:50:04,674] [INFO] Task started: Blastn
[2023-06-29 12:50:04,674] [INFO] Running command: blastn -query GCA_021783525.1_ASM2178352v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bf2c90e-5cb0-480a-a15b-2b53f9ccde4e/dqc_reference/reference_markers_gtdb.fasta -out GCA_021783525.1_ASM2178352v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:50:05,840] [INFO] Task succeeded: Blastn
[2023-06-29 12:50:05,845] [INFO] Selected 9 target genomes.
[2023-06-29 12:50:05,846] [INFO] Target genome list was writen to GCA_021783525.1_ASM2178352v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:50:05,853] [INFO] Task started: fastANI
[2023-06-29 12:50:05,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgd65622e3-ae4b-4ce1-a306-7495274ba95d/GCA_021783525.1_ASM2178352v1_genomic.fna.gz --refList GCA_021783525.1_ASM2178352v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021783525.1_ASM2178352v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:50:10,601] [INFO] Task succeeded: fastANI
[2023-06-29 12:50:10,610] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:50:10,610] [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_000025705.1	s__Sideroxydans lithotrophicus	82.5135	331	518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208015.1	s__Sideroxydans sp016208015	82.207	299	518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235045.1	s__Sideroxydans sp016235045	82.0045	302	518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214695.1	s__Sideroxydans sp016214695	81.9776	293	518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820925.1	s__Sideroxydans sp018820925	81.5789	303	518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.99	99.99	0.96	0.96	2	-
GCA_003445795.1	s__Sideroxydans sp003445795	81.3472	279	518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018813765.1	s__Sideroxydans sp018813765	81.1963	300	518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.93	99.86	0.97	0.93	3	-
GCA_903847155.1	s__Sideroxydans sp903847155	79.6161	227	518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297065.1	s__PALSA-1006 sp004297065	79.3069	204	518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__PALSA-1006	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:50:10,612] [INFO] GTDB search result was written to GCA_021783525.1_ASM2178352v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:50:10,613] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:50:10,616] [INFO] DFAST_QC result json was written to GCA_021783525.1_ASM2178352v1_genomic.fna/dqc_result.json
[2023-06-29 12:50:10,617] [INFO] DFAST_QC completed!
[2023-06-29 12:50:10,617] [INFO] Total running time: 0h0m46s