[2024-01-24 12:47:12,286] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:12,288] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:12,288] [INFO] DQC Reference Directory: /var/lib/cwl/stga839c0c4-615c-44c7-aaa0-7e9eb56ef39d/dqc_reference
[2024-01-24 12:47:13,511] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:13,514] [INFO] Task started: Prodigal
[2024-01-24 12:47:13,514] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2fa8c63-3800-4a3c-a0f6-37e894af3076/GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/cds.fna -a GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:29,468] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:29,468] [INFO] Task started: HMMsearch
[2024-01-24 12:47:29,468] [INFO] Running command: hmmsearch --tblout GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga839c0c4-615c-44c7-aaa0-7e9eb56ef39d/dqc_reference/reference_markers.hmm GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:29,800] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:29,801] [INFO] Found 6/6 markers.
[2024-01-24 12:47:29,845] [INFO] Query marker FASTA was written to GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:47:29,845] [INFO] Task started: Blastn
[2024-01-24 12:47:29,845] [INFO] Running command: blastn -query GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga839c0c4-615c-44c7-aaa0-7e9eb56ef39d/dqc_reference/reference_markers.fasta -out GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:30,704] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:30,746] [INFO] Selected 12 target genomes.
[2024-01-24 12:47:30,747] [INFO] Target genome list was writen to GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:47:30,752] [INFO] Task started: fastANI
[2024-01-24 12:47:30,752] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2fa8c63-3800-4a3c-a0f6-37e894af3076/GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna.gz --refList GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:43,545] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:43,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga839c0c4-615c-44c7-aaa0-7e9eb56ef39d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:43,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga839c0c4-615c-44c7-aaa0-7e9eb56ef39d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:43,556] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:43,557] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:43,557] [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
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	100.0	1749	1752	95	conclusive
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	89.1963	1331	1752	95	below_threshold
Thiocapsa marina	strain=5811	GCA_000223985.2	244573	244573	type	True	88.2917	1260	1752	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	87.4086	1251	1752	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	79.3246	440	1752	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	79.2391	546	1752	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	79.0407	482	1752	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	79.0401	499	1752	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	78.6182	523	1752	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.234	152	1752	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.0243	114	1752	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	75.8961	79	1752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:43,559] [INFO] DFAST Taxonomy check result was written to GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:47:43,560] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:43,560] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:43,561] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga839c0c4-615c-44c7-aaa0-7e9eb56ef39d/dqc_reference/checkm_data
[2024-01-24 12:47:43,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:43,619] [INFO] Task started: CheckM
[2024-01-24 12:47:43,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/checkm_input GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:48:30,085] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:30,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:30,108] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:30,109] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:30,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:48:30,110] [INFO] Task started: Blastn
[2024-01-24 12:48:30,110] [INFO] Running command: blastn -query GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga839c0c4-615c-44c7-aaa0-7e9eb56ef39d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:31,546] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:31,549] [INFO] Selected 7 target genomes.
[2024-01-24 12:48:31,549] [INFO] Target genome list was writen to GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:31,555] [INFO] Task started: fastANI
[2024-01-24 12:48:31,555] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2fa8c63-3800-4a3c-a0f6-37e894af3076/GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna.gz --refList GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:42,081] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:42,090] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:42,090] [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_900106925.1	s__Thiocapsa roseopersicina	100.0	1749	1752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002423035.1	s__Thiocapsa sp002423035	91.045	1068	1752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499735.1	s__Thiocapsa sp001499735	89.7249	1334	1752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399035.1	s__Thiocapsa sp018399035	89.6376	1240	1752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	99.92	99.89	0.99	0.99	3	-
GCA_011390875.1	s__Thiocapsa sp011390875	89.2709	1007	1752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634315.1	s__Thiocapsa rosea	89.1925	1332	1752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000223985.1	s__Thiocapsa marina	88.3181	1257	1752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:42,092] [INFO] GTDB search result was written to GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:42,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:42,095] [INFO] DFAST_QC result json was written to GCF_900106925.1_IMG-taxon_2684622843_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:48:42,095] [INFO] DFAST_QC completed!
[2024-01-24 12:48:42,095] [INFO] Total running time: 0h1m30s