[2024-01-24 12:36:23,378] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:23,380] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:23,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg425952d0-886a-4366-b327-949c5ef9540d/dqc_reference
[2024-01-24 12:36:24,650] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:24,651] [INFO] Task started: Prodigal
[2024-01-24 12:36:24,651] [INFO] Running command: gunzip -c /var/lib/cwl/stg47f995c0-63d0-46c1-bd68-07063dbe81c7/GCF_016583745.1_ASM1658374v1_genomic.fna.gz | prodigal -d GCF_016583745.1_ASM1658374v1_genomic.fna/cds.fna -a GCF_016583745.1_ASM1658374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:33,840] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:33,840] [INFO] Task started: HMMsearch
[2024-01-24 12:36:33,841] [INFO] Running command: hmmsearch --tblout GCF_016583745.1_ASM1658374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg425952d0-886a-4366-b327-949c5ef9540d/dqc_reference/reference_markers.hmm GCF_016583745.1_ASM1658374v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:34,106] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:34,108] [INFO] Found 6/6 markers.
[2024-01-24 12:36:34,136] [INFO] Query marker FASTA was written to GCF_016583745.1_ASM1658374v1_genomic.fna/markers.fasta
[2024-01-24 12:36:34,137] [INFO] Task started: Blastn
[2024-01-24 12:36:34,137] [INFO] Running command: blastn -query GCF_016583745.1_ASM1658374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg425952d0-886a-4366-b327-949c5ef9540d/dqc_reference/reference_markers.fasta -out GCF_016583745.1_ASM1658374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:34,744] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:34,784] [INFO] Selected 30 target genomes.
[2024-01-24 12:36:34,785] [INFO] Target genome list was writen to GCF_016583745.1_ASM1658374v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:34,811] [INFO] Task started: fastANI
[2024-01-24 12:36:34,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f995c0-63d0-46c1-bd68-07063dbe81c7/GCF_016583745.1_ASM1658374v1_genomic.fna.gz --refList GCF_016583745.1_ASM1658374v1_genomic.fna/target_genomes.txt --output GCF_016583745.1_ASM1658374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:53,804] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:53,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg425952d0-886a-4366-b327-949c5ef9540d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:53,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg425952d0-886a-4366-b327-949c5ef9540d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:53,822] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:36:53,822] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:53,822] [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
Chromatium okenii	strain=DSM 169	GCA_016583745.1	61644	61644	type	True	100.0	1002	1010	95	conclusive
Allochromatium warmingii	strain=DSM 173	GCA_900107145.1	61595	61595	type	True	77.3108	162	1010	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	77.1616	66	1010	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	76.9926	136	1010	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	76.9144	138	1010	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.7251	69	1010	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.6873	71	1010	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	76.6014	61	1010	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.5391	85	1010	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	76.4577	102	1010	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	76.4199	53	1010	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	76.3667	88	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:53,825] [INFO] DFAST Taxonomy check result was written to GCF_016583745.1_ASM1658374v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:53,826] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:53,826] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:53,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg425952d0-886a-4366-b327-949c5ef9540d/dqc_reference/checkm_data
[2024-01-24 12:36:53,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:53,864] [INFO] Task started: CheckM
[2024-01-24 12:36:53,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583745.1_ASM1658374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583745.1_ASM1658374v1_genomic.fna/checkm_input GCF_016583745.1_ASM1658374v1_genomic.fna/checkm_result
[2024-01-24 12:37:26,222] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:26,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:26,244] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:26,244] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:26,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583745.1_ASM1658374v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:26,245] [INFO] Task started: Blastn
[2024-01-24 12:37:26,245] [INFO] Running command: blastn -query GCF_016583745.1_ASM1658374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg425952d0-886a-4366-b327-949c5ef9540d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583745.1_ASM1658374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:27,133] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:27,137] [INFO] Selected 20 target genomes.
[2024-01-24 12:37:27,137] [INFO] Target genome list was writen to GCF_016583745.1_ASM1658374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:27,165] [INFO] Task started: fastANI
[2024-01-24 12:37:27,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f995c0-63d0-46c1-bd68-07063dbe81c7/GCF_016583745.1_ASM1658374v1_genomic.fna.gz --refList GCF_016583745.1_ASM1658374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583745.1_ASM1658374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:40,421] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:40,436] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:40,437] [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_016583745.1	s__Chromatium okenii	100.0	1002	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002958735.1	s__Chromatium okenii_A	83.6253	592	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	97.66	97.66	0.81	0.81	2	-
GCF_016583765.1	s__Chromatium weissei	80.2401	483	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897335.1	s__Chromatium sp903897335	77.5047	143	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	99.90	99.90	0.95	0.95	2	-
GCF_900107145.1	s__Allochromatium warmingii	77.2392	166	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012276755.1	s__Marichromatium bheemlicum	77.0253	58	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000227745.2	s__Chromatium violascens	76.9953	135	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342175.1	s__Thiobaca trueperi	76.9314	112	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiobaca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866365.1	s__Chromatium sp903866365	76.851	121	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	76.6873	71	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_000025485.1	s__Allochromatium vinosum	76.2945	101	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:40,439] [INFO] GTDB search result was written to GCF_016583745.1_ASM1658374v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:40,439] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:40,443] [INFO] DFAST_QC result json was written to GCF_016583745.1_ASM1658374v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:40,443] [INFO] DFAST_QC completed!
[2024-01-24 12:37:40,444] [INFO] Total running time: 0h1m17s