[2024-01-25 19:54:05,484] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:05,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:05,498] [INFO] DQC Reference Directory: /var/lib/cwl/stga4dbdeb1-eaff-4ddd-8e8b-583c8747104e/dqc_reference
[2024-01-25 19:54:06,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:06,604] [INFO] Task started: Prodigal
[2024-01-25 19:54:06,604] [INFO] Running command: gunzip -c /var/lib/cwl/stg396a96b3-64eb-4a5c-887d-9a943d01b400/GCF_016583575.1_ASM1658357v1_genomic.fna.gz | prodigal -d GCF_016583575.1_ASM1658357v1_genomic.fna/cds.fna -a GCF_016583575.1_ASM1658357v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:19,222] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:19,222] [INFO] Task started: HMMsearch
[2024-01-25 19:54:19,222] [INFO] Running command: hmmsearch --tblout GCF_016583575.1_ASM1658357v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4dbdeb1-eaff-4ddd-8e8b-583c8747104e/dqc_reference/reference_markers.hmm GCF_016583575.1_ASM1658357v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:19,469] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:19,470] [INFO] Found 6/6 markers.
[2024-01-25 19:54:19,513] [INFO] Query marker FASTA was written to GCF_016583575.1_ASM1658357v1_genomic.fna/markers.fasta
[2024-01-25 19:54:19,514] [INFO] Task started: Blastn
[2024-01-25 19:54:19,514] [INFO] Running command: blastn -query GCF_016583575.1_ASM1658357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4dbdeb1-eaff-4ddd-8e8b-583c8747104e/dqc_reference/reference_markers.fasta -out GCF_016583575.1_ASM1658357v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:20,282] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:20,284] [INFO] Selected 22 target genomes.
[2024-01-25 19:54:20,285] [INFO] Target genome list was writen to GCF_016583575.1_ASM1658357v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:20,334] [INFO] Task started: fastANI
[2024-01-25 19:54:20,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg396a96b3-64eb-4a5c-887d-9a943d01b400/GCF_016583575.1_ASM1658357v1_genomic.fna.gz --refList GCF_016583575.1_ASM1658357v1_genomic.fna/target_genomes.txt --output GCF_016583575.1_ASM1658357v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:41,079] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:41,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4dbdeb1-eaff-4ddd-8e8b-583c8747104e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:41,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4dbdeb1-eaff-4ddd-8e8b-583c8747104e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:41,092] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:54:41,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:54:41,092] [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
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	100.0	1689	1698	95	conclusive
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	81.3414	782	1698	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	81.0367	730	1698	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	81.0288	661	1698	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	80.985	691	1698	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	80.9578	767	1698	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	79.6441	714	1698	95	below_threshold
Thiorhodococcus mannitoliphagus	strain=DSM 18266	GCA_010915725.1	329406	329406	type	True	79.5494	665	1698	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	79.4234	521	1698	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	79.2468	514	1698	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	79.1521	560	1698	95	below_threshold
Thiocapsa marina	strain=5811	GCA_000223985.2	244573	244573	type	True	79.1475	479	1698	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	79.1175	556	1698	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.7731	467	1698	95	below_threshold
Allochromatium warmingii	strain=DSM 173	GCA_900107145.1	61595	61595	type	True	77.9016	162	1698	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.206	201	1698	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.1353	160	1698	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.0761	159	1698	95	below_threshold
Methylocystis heyeri	strain=H2	GCA_004802635.2	391905	391905	type	True	75.7397	52	1698	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	75.2951	72	1698	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	75.2558	101	1698	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:41,093] [INFO] DFAST Taxonomy check result was written to GCF_016583575.1_ASM1658357v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:41,094] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:41,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:41,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4dbdeb1-eaff-4ddd-8e8b-583c8747104e/dqc_reference/checkm_data
[2024-01-25 19:54:41,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:41,147] [INFO] Task started: CheckM
[2024-01-25 19:54:41,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583575.1_ASM1658357v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583575.1_ASM1658357v1_genomic.fna/checkm_input GCF_016583575.1_ASM1658357v1_genomic.fna/checkm_result
[2024-01-25 19:55:18,603] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:18,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:18,621] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:18,622] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:18,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583575.1_ASM1658357v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:18,622] [INFO] Task started: Blastn
[2024-01-25 19:55:18,623] [INFO] Running command: blastn -query GCF_016583575.1_ASM1658357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4dbdeb1-eaff-4ddd-8e8b-583c8747104e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583575.1_ASM1658357v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:19,950] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:19,953] [INFO] Selected 16 target genomes.
[2024-01-25 19:55:19,953] [INFO] Target genome list was writen to GCF_016583575.1_ASM1658357v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:19,970] [INFO] Task started: fastANI
[2024-01-25 19:55:19,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg396a96b3-64eb-4a5c-887d-9a943d01b400/GCF_016583575.1_ASM1658357v1_genomic.fna.gz --refList GCF_016583575.1_ASM1658357v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583575.1_ASM1658357v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:37,311] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:37,322] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:37,322] [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_016583575.1	s__Thiocystis violacea	100.0	1689	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocystis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016653465.1	s__Chromatium minus	81.3357	784	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013385175.1	s__Allochromatium humboldtianum	81.0348	730	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018409545.1	s__Allochromatium tepidum	81.0188	662	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	80.9955	690	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_000227745.2	s__Chromatium violascens	80.9341	768	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866365.1	s__Chromatium sp903866365	80.6916	693	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583565.1	s__Thiorhodococcus violacea_A	80.2987	785	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585215.1	s__Imhoffiella purpurea	80.2764	689	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720725.1	s__Allochromatium palmeri	80.2746	684	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342175.1	s__Thiobaca trueperi	80.2212	638	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiobaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224065.1	s__Imhoffiella drewsii	79.7582	669	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820565.1	s__Thiorhodococcus minor	79.6405	713	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106925.1	s__Thiocapsa roseopersicina	79.4137	522	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	79.1566	560	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_900107145.1	s__Allochromatium warmingii	77.8811	163	1698	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:37,338] [INFO] GTDB search result was written to GCF_016583575.1_ASM1658357v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:37,339] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:37,342] [INFO] DFAST_QC result json was written to GCF_016583575.1_ASM1658357v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:37,342] [INFO] DFAST_QC completed!
[2024-01-25 19:55:37,342] [INFO] Total running time: 0h1m32s